Genes expressed in treated human C3A liver cell cultures

ABSTRACT

The present invention relates to a composition comprising a plurality of cDNAs which are differentially expressed in treated human C3A liver cell cultures and which may be used entirely or in part to diagnose, to stage, to treat, or to monitor the progression or treatment of liver disorders such as hyperlipidemia.

FIELD OF THE INVENTION

[0001] The present invention relates to a composition comprising aplurality of cDNAs which are differentially expressed in treated humanC3A liver cell cultures and which may be used entirely or in part todiagnose, to stage, to treat, or to monitor the progression or treatmentof liver disorders such as hyperlipidemia.

BACKGROUND OF THE INVENTION

[0002] Array technology can provide a simple way to explore theexpression of a single polymorphic gene or the expression profile of alarge number of related or unrelated genes. When the expression of asingle gene is examined, arrays are employed to detect the expression ofa specific gene or its variants. When an expression profile is examined,arrays provide a platform for examining which genes are tissue specific,carrying out housekeeping functions, parts of a signaling cascade, orspecifically related to a particular genetic predisposition, condition,disease, or disorder.

[0003] The potential application of gene expression profiling isparticularly relevant to improving diagnosis, prognosis, and treatmentof disease. For example, both the levels and sequences expressed intissues from subjects with hyperlipidemia may be compared with thelevels and sequences expressed in normal tissue.

[0004] Toxicity testing is a mandatory and time-consuming part of drugdevelopment programs in the pharmaceutical industry. A more rapid screento determine the effects upon metabolism and to detect toxicity of leaddrug candidates may be the use of gene expression microarrays. Forexample, microarrays of various kinds may be produced using full lengthgenes or gene fragments. These arrays can then be used to test samplestreated with the drug candidates to elucidate the gene expressionpattern associated with drug treatment. This gene pattern can becompared with gene expression patterns associated with compounds whichproduce known metabolic and toxicological responses.

[0005] The human C3A cell line is a clonal derivative of HepG2/C3(hepatoma cell line, isolated from a 15-year-old male with liver tumor),which was selected for strong contact inhibition of growth. The use of aclonal population enhances the reproducibility of the cells. C3A cellshave many characteristics of primary human hepatocytes in culture: i)expression of insulin receptor and insulin-like growth factor IIreceptor; ii) secretion of a high ratio of serum albumin compared withα-fetoprotein iii) convertion of ammonia to urea and glutamine; iv)metabolize aromatic amino acids; and v) are able to proliferate inglucose-free and insulin-free medium. The C3A cell line is now wellestablished as an in vitro model of the mature human liver (Mickelson etal. (1995) Hepatology 22:866-875; Nagendra et al. (1997) Am J Physiol272:G408-416).

[0006] Clofibrate is an hypolidemic drug which lowers elevated levels ofserum triglycerides. In rodents, chronic treatment produces hepatomegalyand an increase in hepatic peroxisomes (peroxisome proliferation).Peroxisome proliferators (PPs) are a class of drugs which activate thePP-activated receptor in rodent liver, leading to enzyme induction,stimulation of S-phase, and a suppression of apoptosis (Hasmall andRoberts (1999) Pharmacol. Ther. 82:63-70). PPs include the fibrate classof hypolidemic drugs, phenobarbitone, thiazolidinediones, certainnon-steroidal anti-inflarnmatory drugs, and naturally-occuring fattyacid-derived molecules (Gelman et al. (1999) Cell. Mol. Life Sci.55:932-943). Clofibrate has been shown to increase levels of cytochromeP450 4A. It is also involved in transcription of β-oxidation genes aswell as induction of PP-activated receptors (Kawashima et al. (1997)Arch. Biochem. Biophys. 347:148-154). Peroxisome proliferation that isinduced by both clofibrate and the chemically-related compoundfenofibrate is mediated by a common inhibitory effect on mitochondrialmembrane depolarization (Zhou and Wallace (1999) Toxicol. Sci.48:82-89).

[0007] Captopril is an antihypertensive known as an angiotensinconverting enzyme (ACE) inhibitor. ACE is a target for treatment ofmyocardial infarction and hypotension. ACE inhibitors can be classifiedinto three broad groups based on chemical structure: i)sulfhydryl-containing ACE inhibitors, structurally related to captopril(e.g., fentiapril, pivalo-pril, zofenopril, alacepril); ii)dicarboxyl-containing ACE inhibitors, structurally related to enalapril(e.g., lisinopril, benazepril, quinapril, moexipril, ramipril,spirapril, perindopril, indolapril, pentopril, indala-pril, cilazapril);and iii) phosphorus-containing ACE inhibitors, structurally related tofosinopril. Many ACE inhibitors are ester-containing prodrugs that are100 to 1000 times less potent as ACE inhibitors than their activemetabolites, but have a much better oral bioavailability than the activemolecules. Approximately 16 different ACE inhibitors are usedworld-wide. In general, ACE inhibitors differ with respect to potency;whether ACE inhibition is due to the drug itself or to activation of aprodrug; and pharmacokinetic properties. With the notable exceptions offosinopril and spirapril (which display balanced elimination by theliver and kidneys), ACE inhibitors are cleared predominantly by thekidneys. Drugs that interfere with the renin-angiotensin system play aprominent role in the treatment cardiovascular disease and have beenused as a therapy for a number of diseases including hypotension, leftventricular systolic dysfunction, myocardial infarction, progressiverenal impairment, and scleroderma renal crisis.

[0008] Enalapril is a prodrug that is not highly active and, as such, itmust be hydrolyzed by esterases in the liver to produce the activeparent dicarboxylic acid, enalaprilat. Enalaprilat is a highly potentinhibitor of ACE with a Ki of 0.2 nM but differs from captopril in thatit is an analog of a tripeptide rather than a dipeptide. Enalapril israpidly absorbed when given orally and has an oral bioavailability ofabout 60% (not reduced by food). Although peak concentrations of plasmaenalapril occur within an hour, enalaprilat concentrations do not peakuntil three to four hours. Enalapril has a half-life of only 1.3 hours.However, because it binds tightly to ACE, enalaprilat has a plasmahalf-life of about 11 hours. Nearly all the drug is eliminated by thekidneys either as intact enalapril or enalaprilat.

[0009] Dexamethasone and its derivatives, dexamethasone sodium phosphateand dexamethasone acetate, are synthetic glucocorticoids used asanti-inflammatory or immunosuppressive agents. Dexamethasone has littleto no mineralocorticoid activity and is usually selected for managementof cerebral edema because of its superior ability to penetrate thecentral nervous sytem. Glucocorticoids are naturally occurring hormonesthat prevent or suppress inflammation and immune responses whenadministered at pharmacological doses. Responses can include inhibitionof leukocyte infiltration at the site of inflammation, interference inthe function of mediators of inflammatory response, and suppression ofhumoral immune responses. The anti-inflammatory actions ofcorticosteroids are thought to involve phospholipase A₂ inhibitoryproteins, collectively called lipocortins. The numerous adverse effectsrelated to corticosteroid use usually depend on the dose administeredand the duration of therapy. Proposed mechanisms of action includedecreased IgE synthesis, increased number of β-adrenergic receptors onleukocytes, and decreased arachidonic acid metabolism. During animmediate allergic reaction, such as in chronic bronchial asthma,allergens bridge the IgE antibodies on the surface of mast cells, whichtriggers these cells to release chemotactic substances. Mast cell influxand activation, therefore, is partially responsible for the inflammationand hyperirritability of the oral mucosa in asthmatic patients. Thisinflammation can be retarded by administration of adrenocorticoids. Aswith other corticosteroids, the effects upon liver metabolism andhormone clearance mechanisms are important to understand thepharmacodynamics of a drug.

[0010] Diethylstilbestrol (DES) is used for the palliative treatment ofadvanced, inoperable, metastatic carcinoma of the breast inpost-menopausal women and in men. Estrogens are not used in thetreatment of breast cancer in premenopausal women, because the drugs maystimulate tumor growth rather than inhibit it. In males, DES is used forthe palliative treatment of advanced carcinoma of the prostate; however,the risk of adverse cardiovascular effects of estrogens are alsoconsidered. The specific role of estrogen therapy compared with othertherapies (e.g., orchiectomy, treatment with analogs of gonadotropinreleasing hormone) in the treatment of prostatic cancer has not beenclearly determined. Hormonal manipulation with estrogens currently isconsidered a therapy of choice for patients with inoperable prostatictumors, patients who refuse orchiectomy, and patients whose diseaseprogresses despite orchiectomy in whom the benefits of estrogen use areconsidered to outweigh the risk of adverse effects. As with othersteroid hormones, the effects upon liver metabolism and hormoneclearance mechanisms are important to understand the pharmacodynamics ofa drug.

[0011] The polycyclic aromatic hydrocarbon 3-methylcholanthrene (MCA) isa potent carcinogen that is often used in experimental cancer studies.MCA is also a strong inducer of the cytochrome P450 genes in humans. Inanimal models, MCA induces the upregulation of the cytochrome P450 CYP1Aisoforms in the liver of treated rats.

[0012] Insulin resistance is central to the pathophysiology of type IIdiabetes and a number of other disease states. It has been known forsome time that down-regulation and reduced tyrosine kinase activity ofthe insulin receptor play a role in insulin resistance. However, defectsin the intracellular responses to insulin are also very important, inparticular, tyrosine phosphorylation of the insulin receptor substrate 1(IRS-1) and IRS-1/phosphatidyinositol-3 (PI3) kinase interaction.Despite many advances in the field, understanding of how insulinstimulates glucose transport is fragmentary, in part because the majortargets for insulin signaling to glucose transport is a complex membranetrafficking pathway that is likely to contain many unknown components.Understanding the fundamental physiological response of insulin willhelp to unravel the causes of insulin resistance in type II diabetes.LY294002 is a PI3 kinase-specific inhibitor that promotes cell cyclearrest of C3A cells and promotes differentiation. This inhibitor alsoappears to affect the metabolic activity of the cells, especially withrespect to proteins such as cytochrome P450 molecules.

[0013] The present invention provides for a composition comprising aplurality of cDNAs for use in detecting changes in expression of genesencoding proteins that are associated with treated human C3A liver cellcultures. Such a composition can be employed for the diagnosis,prognosis or treatment of hyperlipidemia and other disorders, such ashypertension, type II diabetes, and tumors of the liver, correlated withdifferential gene expression. The present invention satisfies a need inthe art in that it provides a set of differentially expressed geneswhich may be used entirely or in part to diagnose, to stage, to treat,or to monitor the progression or treatment of a subject with a disordersuch as hyperlipidemia.

SUMMARY

[0014] The present invention provides a composition comprising aplurality of cDNAs and their complements which are differentiallyexpressed in brain tissues and which are selected from SEQ ID NOs:1-401as presented in the Sequence Listing. In one embodiment, each cDNA isdownregulated at least two-fold, SEQ ID NOs:3, 32, 94, 99, 100, 108,137, 196, 274, 299, 380; in another embodiment, each cDNA is upregulatedat least two-fold, SEQ ID NOs:9, 10, 70, 144, 145, 147, 164, 186, 190,191, 203, 271, 305, 344. In one aspect, the composition is useful todiagnose a liver disorder selected from hyperlipidemia, hypertension,type II diabetes, and tumors of the liver. In another aspect, thecomposition is immobilized on a substrate.

[0015] The invention also provides a high throughput method to detectdifferential expression of one or more of the cDNAs of the composition.The method comprises hybridizing the substrate comprising thecomposition with the nucleic acids of a sample, thereby forming one ormore hybridization complexes, detecting the hybridization complexes, andcomparing the hybridization complexes with those of a standard, whereindifferences in the size and signal intensity of each hybridizationcomplex indicates differential expression of nucleic acids in thesample. In one aspect, the sample is from a subject with hyperlipidemiaand differential expression determines an early, mid, and late stage ofthat disorder.

[0016] The invention further provides a high throughput method ofscreening a library or a plurality of molecules or compounds to identifya ligand. The method comprises combining the substrate comprising thecomposition with a library or a plurality of molecules or compoundsunder conditions to allow specific binding and detecting specificbinding, thereby identifying a ligand. The library or a plurality ofmolecules or compounds are selected from DNA molecules, RNA molecules,peptide nucleic acid molecules, mimetics, peptides, transcriptionfactors, repressors, and other regulatory proteins.

[0017] The invention still further provides an isolated cDNA selectedfrom SEQ ID NOs:23, 56, 59, 97, 136, 155, 157, 226, 255, 264, 303, 308,310, 330, 353, 354, 364, 395 as presented in the Sequence Listing. Theinvention also provides a vector comprising the cDNA, a host cellcomprising the vector, and a method for producing a protein comprisingculturing the host cell under conditions for the expression of a proteinand recovering the protein from the host cell culture. The inventionadditionally provides a method for purifying a ligand, the methodcomprising combining a cDNA of the invention with a sample underconditions which allow specific binding, recovering the bound cDNA, andseparating the cDNA from the ligand, thereby obtaining purified ligand.

[0018] The present invention provides a purified protein encoded andproduced by a cDNA of the invention. The invention also provides ahigh-throughput method for using a protein to screen a library or aplurality of molecules or compounds to identify a ligand. The methodcomprises combining the protein or a portion thereof with the library ora plurality of molecules or compounds under conditions to allow specificbinding and detecting specific binding, thereby identifying a ligandwhich specifically binds the protein. A library or a plurality ofmolecules or compounds are selected from DNA molecules, RNA molecules,peptide nucleic acid molecules, mimetics, peptides, proteins, agonists,antagonists, antibodies or their fragments, immunoglobulins, inhibitors,drug compounds, and pharmaceutical agents. The invention furtherprovides for using a protein to purify a ligand. The method comprisescombining the protein or a portion thereof with a sample underconditions to allow specific binding, recovering the bound protein, andseparating the protein from the ligand, thereby obtaining purifiedligand. The invention still further provides a pharmaceuticalcomposition comprising the protein. The invention yet still furtherprovides a method for using the protein to produce an antibody. Themethod comprises immunizing an animal with the protein or anantigenically-effective epitope under conditions to elicit an antibodyresponse, isolating animal antibodies, and screening the isolatedantibodies with the protein to identify an antibody which specificallybinds the protein. The invention yet still further provides a method forusing the protein to purify antibodies which bind specifically to theprotein.

[0019] The invention also provides a purified protein selected from SEQID NOs: 158, 311, 331.

DESCRIPTION OF THE SEQUENCE LISTING AND TABLES

[0020] A portion of the disclosure of this patent document containsmaterial that is subject to copyright protection. The copyright ownerhas no objection to the facsimile reproduction by anyone of the patentdocument or the patent disclosure, as it appears in the Patent andTrademark Office patent file or records, but otherwise reserves allcopyright rights whatsoever.

[0021] The Sequence Listing is a compilation of cDNAs obtained bysequencing and extension of clone inserts. Each sequence is identifiedby a sequence identification number (SEQ ID NO) and by the templatenumber (TEMPLATE ID) from which it was obtained.

[0022] Table 1 lists the differential expression levels of cDNA as afunction of the increase or decreased levels compared with levels inuntreated human C3A liver cell cultures. Column 1 lists the clonepresent on the array (CLONE ID). Columns 2 through 10 list the compoundused to treat the cell cultures, Clofibrate, Fenofibrate, Captopril,Enalapril, Dexamethasone, diethylstilbestrol (DES) 3-methylcholanthrene(MCA), LY294002, or insulin together with LY294002 (INS/LY294002),respectively.

[0023] Table 2 shows the nucleotide template sequence corresponding tothe encoded protein template and to the clone present on the microarray.Columns 1, 2, 3, 4, and 5 show the clone number (CLONE ID), nucleotideSEQ ID NO, nucleotide TEMPLATE ID, protein SEQ ID NO, and proteinTEMPLATE ID, respectively. Template IDs with the suffix ‘c’ read on thecomplementary nucleotide strand.

[0024] Table 3 lists the functional annotation of the cDNAs of thepresent invention. Columns 1 and 2 show the SEQ ID NO and TEMPLATE ID,respectively. Columns 3, 4, and 5 show the GenBank hit (GI Number),probability score (E-value), and functional annotation, respectively, asdetermined by BLAST analysis (version 1.4 using default parameters;Altschul (1993) J Mol Evol 36: 290-300; Altschul et al. (1990) J MolBiol 215:403410) of the cDNA against GenBank (release 116; NationalCenter for Biotechnology Information (NCBI), Bethesda Md).

[0025] Table 4 shows Pfam annotations of the cDNAs of the presentinvention. Columns 1 and 2 show the SEQ ID NO and TEMPLATE ID,respectively. Columns 3, 4, and 5 show the first residue (START), lastresidue (STOP), and reading frame (FRAME), respectively, for the segmentof the cDNA identified by Pfam analysis. Columns 6, 7, and 8 show thePfam ID, Pfam description, and E-values, respectively, corresponding tothe polypeptide domain encoded by the cDNA segment.

[0026] Table 5 shows signal peptide and transmembrane regions predictedwithin the cDNAs of the present invention. Columns 1 and 2 show the SEQID NO and TEMPLATE ID, respectively. Columns 3, 4, and 5 show the firstresidue (START), last residue (STOP), and reading frame (FRAME),respectively, for a segment of the cDNA, and column 6 (HIT TYPE)identifies the polypeptide encoded by the segment as either a signalpeptide (SP) or transmembrane (TM) domain.

[0027] Table 6 shows the region of each cDNA encompassed by the clonepresent on a microarray and identified as differentially expressed.Columns 1 and 2 show the SEQ ID NO and TEMPLATE ID, respectively. Column3 shows the CLONE ID and columns 4 and 5 show the first residue (START)and last residue (STOP) encompassed by the clone on the template.

[0028] Table 7 lists the tissue distribution of the nucleotidetemplates. Columns 1 and 2 list the SEQ ID NO and TEMPLATE ID,respectively. Column 3 lists the predominant tissue distribution (TISSUEDISTRIBUTION) as a percentage of total tissues in the Incyte LIFESEQGOLD database (Incyte Genomics, Palo Alto Calif.).

DESCRIPTION OF THE INVENTION

[0029] Definitions

[0030] “Array” refers to an ordered arrangement of at least two cDNAs ona substrate. At least one of the cDNAs represents a control or standardsequence, and the other, a cDNA of diagnostic interest. The arrangementof from about two to about 40,000 cDNAs on the substrate assures thatthe size and signal intensity of each labeled hybridization complexformed between a cDNA and a sample nucleic acid is individuallydistinguishable.

[0031] The “complement” of a nucleic acid molecule of the SequenceListing refers to a cDNA which is completely complementary over the fulllength of the sequence and which will hybridize to the nucleic acidmolecule under conditions of high stringency.

[0032] A “composition” comprises at least two and up to 401 sequences ofthe Sequence Listing. “cDNA” refers to a chain of nucleotides, anisolated polynucleotide, nucleic acid molecule, or any fragment orcomplement thereof. It may have originated recombinantly orsynthetically, be double-stranded or single-stranded, coding and/ornoncoding, an exon with or without an intron from a genomic DNAmolecule, and purified or combined with carbohydrate, lipids, protein orinorganic elements or substances. Preferably, the cDNA is from about4000 to about 5000 nucleotides.

[0033] The phrase “cDNA encoding a protein” refers to a nucleic acidsequence that closely aligns with sequences which encode conservedregions, motifs or domains that were identified by employing analyseswell known in the art. These analyses include BLAST (Basic LocalAlignment Search Tool; Altschul (1993) J Mol Evol 36: 290-300; Altschulet al. (1990) J Mol Biol 215:403-410) which provides identity within theconserved region. Brenner et al. (1998; Proc Natl Acad Sci 95:6073-6078)who analyzed BLAST for its ability to identify structural homologs bysequence identity found 30% identity is a reliable threshold forsequence alignments of at least 150 residues and 40% is a reasonablethreshold for alignments of at least 70 residues (Brenner et al., page6076, column 2).

[0034] “Derivative” refers to a cDNA or a protein that has beensubjected to a chemical modification. Derivatization of a cDNA caninvolve substitution of a nontraditional base such as queosine or of ananalog such as hypoxanthine. These substitutions are well known in theart. Derivatization of a protein involves the replacement of a hydrogenby an acetyl, acyl, alkyl, amino, formyl, or morpholino group.Derivative molecules retain the biological activities of the naturallyoccurring molecules but may confer advantages such as longer lifespan orenhanced activity.

[0035] “Differential expression” refers to an increased, upregulated orpresent, or decreased, downregulated or absent, gene expression asdetected by the absence, presence, or at least two-fold changes in theamount of transcribed messenger RNA or translated protein in a sample.

[0036] “Disorder” refers to conditions, diseases or syndromes of theliver, including hyperlipidemia, hypertension, type II diabetes, tumorsof the liver, and disorders of the inflammatory and immune response.

[0037] “Fragment” refers to a chain of consecutive nucleotides fromabout 200 to about 700 base pairs in length. Fragments may be used inPCR or hybridization technologies to identify related nucleic acidmolecules and in binding assays to screen for a ligand. Nucleic acidsand their ligands identified in this manner are useful as therapeuticsto regulate replication, transcription or translation.

[0038] A “hybridization complex” is formed between a cDNA and a nucleicacid of a sample when the purines of one molecule hydrogen bond with thepyrimidines of the complementary molecule, e.g., 5′-A-G-T-C-3′ basepairs with 3′-T-C-A-G-5′. The degree of complementarity and the use ofnucleotide analogs affect the efficiency and stringency of hybridizationreactions.

[0039] “Ligand” refers to any agent, molecule, or compound which willbind specifically to a complementary site on a cDNA molecule orpolynucleotide, or to an epitope or a protein. Such ligands stabilize ormodulate the activity of polynucleotides or proteins and may be composedof inorganic or organic substances including nucleic acids, proteins,carbohydrates, fats, and lipids.

[0040] “Oligonucleotide” refers a single stranded molecule from about 18to about 60 nucleotides in length which may be used in hybridization oramplification technologies or in regulation of replication,transcription or translation. Substantially equivalent terms areamplimer, primer, and oligomer.

[0041] “Portion” refers to any part of a protein used for any purpose;but especially, to an epitope for the screening of ligands or for theproduction of antibodies.

[0042] “Post-translational modification” of a protein can involve lipidation, glycosylation, phosphorylation, acetylation, racemization,proteolytic cleavage, and the like. These processes may occursynthetically or biochemically. Biochemical modifications will vary bycellular location, cell type, pH, enzymatic milieu, and the like.

[0043] “Probe” refers to a cDNA that hybridizes to at least one nucleicacid molecule in a sample. Where targets are single stranded, probes arecomplementary single strands. Probes can be labeled with reportermolecules for use in hybridization reactions including Southern,northern, in situ, dot blot, array, and like technologies or inscreening assays.

[0044] “Protein” refers to a polypeptide or any portion thereof. A“portion” of a protein retains at least one biological or antigeniccharacteristic of a native protein. An “oligopeptide” is an amino acidsequence from about five residues to about 15 residues that is used aspart of a fusion protein to produce an antibody.

[0045] “Purified” refers to any molecule or compound that is separatedfrom its natural environment and is from about 60% free to about 90%free from other components with which it is naturally associated.

[0046] “Sample” is used in its broadest sense as containing nucleicacids, proteins, antibodies, and the like. A sample may comprise abodily fluid; the soluble fraction of a cell preparation, or an aliquotof media in which cells were grown; a chromosome, an organelle, ormembrane isolated or extracted from a cell; genomic DNA, RNA, or cDNA insolution or bound to a substrate; a cell; a tissue; a tissue print; afingerprint, buccal cells, skin, or hair; and the like.

[0047] “Specific binding” refers to a special and precise interactionbetween two molecules which is dependent upon their structure,particularly their molecular side groups. For example, the intercalationof a regulatory protein into the major groove of a DNA molecule, thehydrogen bonding along the backbone between two single stranded nucleicacids, or the binding between an epitope of a protein and an agonist,antagonist, or antibody.

[0048] “Similarity” as applied to sequences, refers to thequantification (usually percentage) of nucleotide or residue matchesbetween at least two sequences aligned using a standardized algorithmsuch as Smith-Waterman alignment (Smith and Waterman (1981) J Mol Biol147:195-197) or BLAST2 (Altschul et al. (1997) Nucleic Acids Res25:3389-3402). BLAST2 may be used in a standardized and reproducible wayto insert gaps in one of the sequences in order to optimize alignmentand to achieve a more meaningful comparison between them.

[0049] “Substrate” refers to any rigid or semi-rigid support to whichcDNAs or proteins are bound and includes membranes, filters, chips,slides, wafers, fibers, magnetic or nonmagnetic beads, gels, capillariesor other tubing, plates, polymers, and microparticles with a variety ofsurface forms including wells, trenches, pins, channels and pores.

[0050] “Variant” refers to molecules that are recognized variations of acDNA or a protein encoded by the cDNA. Splice variants may be determinedby BLAST score, wherein the score is at least 100, and most preferablyat least 400. Allelic variants have a high percent identity to the cDNAsand may differ by about three bases per hundred bases. “Singlenucleotide polymorphism” (SNP) refers to a change in a single base as aresult of a substitution, insertion or deletion. The change may beconservative (purine for purine) or non-conservative (purine topyrimidine) and may or may not result in a change in an encoded aminoacid.

[0051] The Invention

[0052] The present invention provides for a composition comprising aplurality of cDNAs or their complements, SEQ ID NOs: 1-401 which may beused on a substrate to diagnose, to stage, to treat or to monitor theprogression or treatment of a liver disorder. These cDNAs representknown and novel genes differentially expressed in C3A liver cellstreated with clofibrate, fenofibrate, captopril, enalapril,dexamethasone, diethylstilbestrol (DES) 3-methylcholanthrene (MCA),LY294002, or insulin together with LY294002. The composition may be usedin its entirety or in part, as subsets of cDNAs downregulated byfibrates, SEQ ID NOs:3, 32, 94, 137, 196, 274, and 380; of cDNAsupregulated by fibrates SEQ ID NOs:9, 10, 70, 147, 164, 186, 190, 191,203, 271, and 344; of cDNAs downregulated by captopril, enalapril, anddexamethasone SEQ ID NOs:3, 99, 100, 108, and 299; and of cDNAsupregulated by captopril, enalapril, and dexamethasone SEQ ID NOs:9, 10,70, 144, 145, 190, 203, 271, and 305. SEQ ID NOs:23, 56, 59, 97, 136,155, 157, 226, 255, 264, 303, 308, 310, 330, 353, 354, 364, and 395represent novel cDNAs associated with treatment of human C3A livercells. Since the novel cDNAs were identified solely by theirdifferential expression, it is not essential to know a priori the name,structure, or function of the gene or the protein encoded thereby. Theusefulness of the novel cDNAs exists in their immediate value asdiagnostics for disorders of liver metabolism and tumors of the liver.

[0053] The invention also provides isolated proteins SEQ ID NOs: 158,311, 331 which are encoded by the cDNAs of SEQ ID NOs:157, 310, 330 asshown in Table 2.

[0054] Table 1 shows those genes on the array having differentialexpression (two-fold or greater increase or decrease) in treated humanC3A liver cell cultures. Column 1 shows the clone ID and columns 2through 10 show the measured expression levels of the cDNA in C3A cellstreated with clofibrate, fenofibrate, captopril, enalapril,dexamethasone, diethylstilbestrol (DES) 3-methyl-cholanthrene (MCA),LY294002, and insulin together with LY294002, respectively. Table 2shows the nucleotide template sequences and the respective encodedproteins sequences which correspond to the upregulated or downregulatedclones present on the array. Table 3 shows the functional annotation ofthe template cDNAs as determined by BLAST analysis. Table 4 shows thefunctional annotation as determined by Pfam analysis. Table 5 shows thefunctional annotation as determined by Hidden Markov Model analysis forsignal peptide or for transmembrane regions, column 6:SP or TM,respectively. Table 6 shows the positional information of the clonepresent on the array relative to the nucleotide template sequence. Table7 shows the tissue distribution of the nucleotide template sequences.

[0055] The cDNAs of the invention define a differential expressionpattern against which to compare the expression pattern of biopsiedand/or in vitro treated human liver tissues. Experimentally,differential expression of the cDNAs can be evaluated by methodsincluding, but not limited to, differential display by spatialimmobilization or by gel electrophoresis, genome mismatch scanning,representational discriminant analysis, clustering, transcript imagingand array technologies. These methods may be used alone or incombination.

[0056] The composition may be arranged on a substrate and hybridizedwith tissues from subjects with diagnosed liver disorders to identifythose sequences which are differentially expressed in bothhyperlipidemia and other liver disorders. This allows identification ofthose sequences of highest diagnostic and potential therapeutic value.In one embodiment, an additional set of cDNAs, such as cDNAs encodingsignaling molecules, are arranged on the substrate with the composition.Such combinations may be useful in the elucidation of pathways which areaffected in a particular liver disorder or to identify new, coexpressed,candidate, therapeutic molecules.

[0057] In another embodiment, the composition can be used for largescale genetic or gene expression analysis of a large number of novel,nucleic acid molecules. These samples are prepared by methods well knownin the art and are from mammalian cells or tissues which are in acertain stage of development; have been treated with a known molecule orcompound, such as a cytokine, growth factor, a drug, and the like; orhave been extracted or biopsied from a mammal with a known or unknowncondition, disorder, or disease before or after treatment. The samplenucleic acid molecules are hybridized to the composition for the purposeof defining a novel gene profile associated with that developmentalstage, treatment, or disorder.

[0058] cDNAs and Their Uses

[0059] cDNAs can be prepared by a variety of synthetic or enzymaticmethods well known in the art. cDNAs can be synthesized, in whole or inpart, using chemical methods well known in the art (Caruthers et al.(1980) Nucleic Acids Symp. Ser. (7)215-233). Alternatively, cDNAs can beproduced enzymatically or recombinantly, by in vitro or in vivotranscription.

[0060] Nucleotide analogs can be incorporated into cDNAs by methods wellknown in the art. The only requirement is that the incorporated analogmust base pair with native purines or pyrimidines. For example,2,6-diaminopurine can substitute for adenine and form stronger bondswith thymidine than those between adenine and thymidine. A weaker pairis formed when hypoxanthine is substituted for guanine and base pairswith cytosine. Additionally, cDNAs can include nucleotides that havebeen derivatized chemically or enzymatically.

[0061] cDNAs can be synthesized on a substrate. Synthesis on the surfaceof a substrate may be accomplished using a chemical coupling procedureand a piezoelectric printing apparatus as described by Baldeschweiler etal. (PCT publication WO95/251116). Alternatively, the cDNAs can besynthesized on a substrate surface using a self-addressable electronicdevice that controls when reagents are added as described by Heller etal. (U.S. Pat. No. 5,605,662). cDNAs can be synthesized directly on asubstrate by sequentially dispensing reagents for their synthesis on thesubstrate surface or by dispensing preformed DNA fragments to thesubstrate surface. Typical dispensers include a micropipette deliveringsolution to the substrate with a robotic system to control the positionof the micropipette with respect to the substrate. There can be amultiplicity of dispensers so that reagents can be delivered to thereaction regions efficiently.

[0062] cDNAs can be immobilized on a substrate by covalent means such asby chemical bonding procedures or UV irradiation. In one method, a cDNAis bound to a glass surface which has been modified to contain epoxideor aldehyde groups. In another method, a cDNA is placed on a polylysinecoated surface and UV cross-linked to it as described by Shalon et al.(WO95/35505). In yet another method, a cDNA is actively transported froma solution to a given position on a substrate by electrical means(Heller, supra). cDNAs do not have to be directly bound to thesubstrate, but rather can be bound to the substrate through a linkergroup. The linker groups are typically about 6 to 50 atoms long toprovide exposure of the attached cDNA. Preferred linker groups includeethylene glycol oligomers, diamines, diacids and the like. Reactivegroups on the substrate surface react with a terminal group of thelinker to bind the linker to the substrate. The other terminus of thelinker is then bound to the cDNA. Alternatively, polynucleotides,plasmids or cells can be arranged on a filter. In the latter case, cellsare lysed, proteins and cellular components degraded, and the DNA iscoupled to the filter by UV cross-linking.

[0063] The cDNAs may be used for a variety of purposes. For example, thecomposition of the invention may be used on an array. The array, inturn, can be used in high-throughput methods for detecting a relatedpolynucleotide in a sample, screening a plurality of molecules orcompounds to identify a ligand, diagnosing a liver disorder, orinhibiting or inactivating a therapeutically relevant gene related tothe cDNA.

[0064] When the cDNAs of the invention are employed on a microarray, thecDNAs are arranged in an ordered fashion so that each cDNA is present ata specified location. Because the cDNAs are at specified locations onthe substrate, the hybridization patterns and intensities, whichtogether create a unique expression profile, can be interpreted in termsof expression levels of particular genes and can be correlated with aparticular metabolic process, condition, disorder, disease, stage ofdisease, or treatment.

[0065] Hybridization

[0066] The cDNAs or fragments or complements thereof may be used invarious hybridization technologies. The cDNAs may be labeled using avariety of reporter molecules by either PCR , recombinant, or enzymatictechniques. For example, a commercially available vector containing thecDNA is transcribed in the presence of an appropriate polymerase, suchas T7 or SP6 polymerase, and at least one labeled nucleotide. Commercialkits are available for labeling and cleanup of such cDNAs. Radioactive(Amersham Pharmacia Biotech (APB), Piscataway N.J.), fluorescent (OperonTechnologies, Alameda Calif.), and chemiluminescent labeling (Promega,Madison Wis.) are well known in the art.

[0067] A cDNA may represent the complete coding region of an MRNA or bedesigned or derived from unique regions of the mRNA or genomic molecule,an intron, a 3′ untranslated region, or from a conserved motif. The cDNAis at least 18 contiguous nucleotides in length and is usually singlestranded. Such a cDNA may be used under hybridization conditions thatallow binding only to an identical sequence, a naturally occurringmolecule encoding the same protein, or an allelic variant. Discovery ofrelated human and mammalian sequences may also be accomplished using apool of degenerate cDNAs and appropriate hybridization conditions.Generally, a cDNA for use in Southern or northern hybridizations may befrom about 400 to about 6000 nucleotides long. Such cDNAs have highbinding specificity in solution-based or substrate-based hybridizations.An oligonucleotide, a fragment of the cDNA, may be used to detect apolynucleotide in a sample using PCR.

[0068] The stringency of hybridization is determined by G+C content ofthe cDNA, salt concentration, and temperature. In particular, stringencyis increased by reducing the concentration of salt or raising thehybridization temperature. In solutions used for some membrane basedhybridizations, addition of an organic solvent such as formamide allowsthe reaction to occur at a lower temperature. Hybridization may beperformed with buffers, such as 5×saline sodium citrate (SSC) with 1%sodium dodecyl sulfate (SDS) at 60° C., that permit the formation of ahybridization complex between nucleic acid sequences that contain somemismatches. Subsequent washes are performed with buffers such as 0.2×SSCwith 0.1% SDS at either 45° C. (medium stringency) or 65°-68° C. (highstringency). At high stringency, hybridization complexes will remainstable only where the nucleic acid molecules are completelycomplementary. In some membrane-based hybridizations, preferably 35% ormost preferably 50%, formamide may be added to the hybridizationsolution to reduce the temperature at which hybridization is performed.Background signals may be reduced by the use of detergents such asSarkosyl or Triton X-100 (Sigma Aldrich, St. Louis Mo.) and a blockingagent such as denatured salmon sperm DNA. Selection of components andconditions for hybridization are well known to those skilled in the artand are reviewed in Ausubel et al. (1997, Short Protocols in MolecularBiology, John Wiley & Sons, New York N.Y., Units 2.8-2.11, 3.18-3.19 and4-64.9).

[0069] Dot-blot, slot-blot, low density and high density arrays areprepared and analyzed using methods known in the art. cDNAs from about18 consecutive nucleotides to about 5000 consecutive nucleotides inlength are contemplated by the invention and used in array technologies.The preferred number of cDNAs on an array is at least about 100,000, amore preferred number is at least about 40,000, an even more preferrednumber is at least about 10,000, and a most preferred number is at leastabout 600 to about 800. The array may be used to monitor the expressionlevel of large numbers of genes simultaneously and to identify geneticvariants, mutations, and SNPs. Such information may be used to determinegene function; to understand the genetic basis of a disorder; todiagnose a disorder; and to develop and monitor the activities oftherapeutic agents being used to control or cure a disorder. (See, e.g.,U.S. Pat. No. 5,474,796; WO95/11995; WO95/35505; U.S. Pat. No.5,605,662; and U.S. Pat. No. 5,958,342.)

[0070] Screening and Purification Assays

[0071] A cDNA may be used to screen a library or a plurality ofmolecules or compounds for a ligand which specifically binds the cDNA.Ligands may be DNA molecules, RNA molecules, peptide nucleic acidmolecules, peptides, proteins such as transcription factors, promoters,enhancers, repressors, and other proteins that regulate replication,transcription, or translation of the polynucleotide in the biologicalsystem. The assay involves combining the cDNA or a fragment thereof withthe molecules or compounds under conditions that allow specific bindingand detecting the bound cDNA to identify at least one ligand thatspecifically binds the cDNA.

[0072] In one embodiment, the cDNA may be incubated with a library ofisolated and purified molecules or compounds and binding activitydetermined by methods such as a gel-retardation assay (U.S. Pat. No.6,010,849) or a reticulocyte lysate transcriptional assay. In anotherembodiment, the cDNA may be incubated with nuclear extracts frombiopsied and/or cultured cells and tissues. Specific binding between thecDNA and a molecule or compound in the nuclear extract is initiallydetermined by gel shift assay. Protein binding may be confirmed byraising antibodies against the protein and adding the antibodies to thegel-retardation assay where specific binding will cause a supershift inthe assay.

[0073] In another embodiment, the cDNA may be used to purify a moleculeor compound using affinity chromatography methods well known in the art.In one embodiment, the cDNA is chemically reacted with cyanogen bromidegroups on a polymeric resin or gel. Then a sample is passed over andreacts with or binds to the cDNA. The molecule or compound which isbound to the cDNA may be released from the cDNA by increasing the saltconcentration of the flow-through medium and collected.

[0074] The cDNA may be used to purify a ligand from a sample. A methodfor using a cDNA to purify a ligand would involve combining the cDNA ora fragment thereof with a sample under conditions to allow specificbinding, recovering the bound cDNA, and using an appropriate agent toseparate the cDNA from the purified ligand.

[0075] Protein Production and Uses

[0076] The full length cDNAs or fragment thereof may be used to producepurified proteins using recombinant DNA technologies described hereinand taught in Ausubel et al. (supra; Units 16.1-16.62). One of theadvantages of producing proteins by these procedures is the ability toobtain highly-enriched sources of the proteins thereby simplifyingpurification procedures.

[0077] The proteins may contain amino acid substitutions, deletions orinsertions made on the basis of similarity in polarity, charge,solubility, hydrophobicity, hydrophilicity, and/or the amphipathicnature of the residues involved. Such substitutions may be conservativein nature when the substituted residue has structural or chemicalproperties similar to the original residue (e.g., replacement of leucinewith isoleucine or valine) or they may be nonconservative when thereplacement residue is radically different (e.g., a glycine replaced bya tryptophan). Computer programs included in LASERGENE software(DNASTAR, Madison Wis.), MACVECTOR software (Genetics Computer Group,Madison Wis.) and RasMol software (www.umass.edu/microbio/rasmol) may beused to help determine which and how many amino acid residues in aparticular portion of the protein may be substituted, inserted, ordeleted without abolishing biological or immunological activity.

[0078] Expression of Encoded Proteins

[0079] Expression of a particular cDNA may be accomplished by cloningthe cDNA into a vector and transforming this vector into a host cell.The cloning vector used for the construction of cDNA libraries in theLIFESEQ databases may also be used for expression. Such vectors usuallycontain a promoter and a polylinker useful for cloning, priming, andtranscription. An exemplary vector may also contain the promoter forβ-galactosidase, an amino-terminal methionine and the subsequent sevenamino acid residues of β-galactosidase. The vector may be transformedinto competent E. coli cells. Induction of the isolated bacterial strainwith isopropylthiogalactoside (IPTG) using standard methods will producea fusion protein that contains an N terminal methionine, the first sevenresidues of β-galactosidase, about 15 residues of linker, and theprotein encoded by the cDNA.

[0080] The cDNA may be shuttled into other vectors known to be usefulfor expression of protein in specific hosts. Oligonucleotides containingcloning sites and fragments of DNA sufficient to hybridize to stretchesat both ends of the cDNA may be chemically synthesized by standardmethods. These primers may then be used to amplify the desired fragmentsby PCR. The fragments may be digested with appropriate restrictionenzymes under standard conditions and isolated using gelelectrophoresis. Alternatively, similar fragments are produced bydigestion of the cDNA with appropriate restriction enzymes and filled inwith chemically synthesized oligonucleotides. Fragments of the codingsequence from more than one gene may be ligated together and expressed.

[0081] Signal sequences that dictate secretion of soluble proteins areparticularly desirable as component parts of a recombinant sequence. Forexample, a chimeric protein may be expressed that includes one or moreadditional purification-facilitating domains. Such domains include, butare not limited to, metal-chelating domains that allow purification onimmobilized metals, protein A domains that allow purification onimmobilized immunoglobulin, and the domain utilized in the FLAGSextension/affinity purification system (Immunex, Seattle Wash.). Theinclusion of a cleavable-linker sequence such as ENTEROKINASEMAX(Invitrogen, San Diego Calif.) between the protein and the purificationdomain may also be used to recover the protein.

[0082] Suitable host cells may include, but are not limited to,mammalian cells such as Chinese Hamster Ovary (CHO) and human 293 cells,insect cells such as Sf9 cells, plant cells such as Nicotiana tabacum,yeast cells such as Saccharomvces cerevisiae, and bacteria such as E.coli. For each of these cell systems, a useful vector may also includean origin of replication and one or two selectable markers to allowselection in bacteria as well as in a transformed eukaryotic host.Vectors for use in eukaryotic host cells may require the addition of 3′poly(A) tail if the cDNA lacks poly(A).

[0083] Additionally, the vector may contain promoters or enhancers thatincrease gene expression. Many promoters are known and used in the art.Most promoters are host specific and exemplary promoters includes SV40promoters for CHO cells; T7 promoters for bacterial hosts; viralpromoters and enhancers for plant cells; and PGH promoters for yeast.Adenoviral vectors with the rous sarcoma virus enhancer or retroviralvectors with long terminal repeat promoters may be used to drive proteinexpression in mammalian cell lines. Once homogeneous cultures ofrecombinant cells are obtained, large quantities of secreted solubleprotein may be recovered from the conditioned medium and analyzed usingchromatographic methods well known in the art. An alternative method forthe production of large amounts of secreted protein involves thetransformation of mammalian embryos and the recovery of the recombinantprotein from milk produced by transgenic cows, goats, sheep, and thelike.

[0084] In addition to recombinant production, proteins or portionsthereof may be produced manually, using solid-phase techniques (Stewartet al. (1969) Solid-Phase Peptide Synthesis, W H Freeman, San FranciscoCalif.; Merrifield (1963) J Am Chem Soc 5:2149-2154), or using machinessuch as the ABI431A peptide synthesizer (Applied Biosystems, Foster CityCalif.). Proteins produced by any of the above methods may be used aspharmaceutical compositions to treat disorders associated with null orinadequate expression of the genomic sequence.

[0085] Screening and Purification Assays

[0086] A protein or a portion thereof encoded by the cDNA may be used toscreen a library or a plurality of molecules or compounds for a ligandwith specific binding affinity or to purify a molecule or compound froma sample. The protein or portion thereof employed in such screening maybe free in solution, affixed to an abiotic or biotic substrate, orlocated intracellularly. For example, viable or fixed prokaryotic hostcells that are stably transformed with recombinant nucleic acids thathave expressed and positioned a protein on their cell surface can beused in screening assays. The cells are screened against a library or aplurality of ligands and the specificity of binding or formation ofcomplexes between the expressed protein and the ligand may be measured.The ligands may be DNA, RNA, or PNA molecules, agonists, antagonists,antibodies, immunoglobulins, inhibitors, peptides, pharmaceuticalagents, proteins, drugs, or any other test molecule or compound thatspecifically binds the protein. An exemplary assay involves combiningthe mammalian protein or a portion thereof with the molecules orcompounds under conditions that allow specific binding and detecting thebound protein to identify at least one ligand that specifically bindsthe protein.

[0087] This invention also contemplates the use of competitive drugscreening assays in which neutralizing antibodies capable of binding theprotein specifically compete with a test compound capable of binding tothe protein or oligopeptide or fragment thereof. One method for highthroughput screening using very small assay volumes and very smallamounts of test compound is described in U.S. Pat. No. 5,876,946.Molecules or compounds identified by screening may be used in a modelsystem to evaluate their toxicity, diagnostic, or therapeutic potential.

[0088] The protein may be used to purify a ligand from a sample. Amethod for using a protein to purify a ligand would involve combiningthe protein or a portion thereof with a sample under conditions to allowspecific binding, recovering the bound protein, and using an appropriatechaotropic agent to separate the protein from the purified ligand.

[0089] Production of Antibodies

[0090] A protein encoded by a cDNA of the invention may be used toproduce specific antibodies. Antibodies may be produced using anoligopeptide or a portion of the protein with inherent immunologicalactivity. Methods for producing antibodies include: 1) injecting ananimal, usually goats, rabbits, or mice, with the protein, or anantigenically-effective portion or an oligopeptide thereof, to induce animmune response; 2) engineering hybridomas to produce monoclonalantibodies; 3) inducing in vivo production in the lymphocyte population;or 4) screening libraries of recombinant immunoglobulins. Recombinantimmunoglobulins may be produced as taught in U.S. Pat. No. 4,816,567.

[0091] Antibodies produced using the proteins of the invention areuseful for the diagnosis of prepathologic disorders as well as thediagnosis of chronic or acute diseases characterized by abnormalities inthe expression, amount, or distribution of the protein. A variety ofprotocols for competitive binding or immunoradiometric assays usingeither polyclonal or monoclonal antibodies specific for proteins arewell known in the art. Immunoassays typically involve the formation ofcomplexes between a protein and its specific binding molecule orcompound and the measurement of complex formation. Immunoassays mayemploy a two-site, monoclonal-based assay that utilizes monoclonalantibodies reactive to two noninterfering epitopes on a specific proteinor a competitive binding assay (Pound (1998) Immunochemical Protocols,Humana Press, Totowa N.J.).

[0092] Immunoassay procedures may be used to quantify expression of theprotein in cell cultures, in subjects with a particular disorder or inmodel animal systems under various conditions. Increased or decreasedproduction of proteins as monitored by immunoassay may contribute toknowledge of the cellular activities associated with developmentalpathways, engineered conditions or diseases, or treatment efficacy. Thequantity of a given protein in a given tissue may be determined byperforming immunoassays on freeze-thawed detergent extracts ofbiological samples and comparing the slope of the binding curves tobinding curves generated by purified protein.

[0093] Labeling of Molecules for Assay

[0094] A wide variety of reporter molecules and conjugation techniquesare known by those skilled in the art and may be used in various cDNA,polynucleotide, protein, peptide or antibody assays. Synthesis oflabeled molecules may be achieved using commercial kits forincorporation of a labeled nucleotide such as ³²P-dCTP, Cy3-dCTP orCy5-dCTP or amino acid such as ³⁵S-methionine. Polynucleotides, cDNAs,proteins, or antibodies may be directly labeled with a reporter moleculeby chemical conjugation to amines, thiols and other groups present inthe molecules using reagents such as BIODIPY or FITC (Molecular Probes,Eugene Oreg.).

[0095] The proteins and antibodies may be labeled for purposes of assayby joining them, either covalently or noncovalently, with a reportermolecule that provides for a detectable signal. A wide variety of labelsand conjugation techniques are known and have been reported in thescientific and patent literature including, but not limited to U.S. Pat.No. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149;and 4,366,241.

[0096] DIAGNOSTICS

[0097] The cDNAs, or fragments thereof, may be used to detect andquantify differential gene expression; absence, presence, or excessexpression of mRNAs; or to monitor mRNA levels during therapeuticintervention. Disorders associated with altered expression includehyperlipidemia, hypertension, type II diabetes, and tumors of the liver.These cDNAs can also be utilized as markers of treatment efficacyagainst the disorders noted above and other liver disorders, conditions,and diseases over a period ranging from several days to months. Thediagnostic assay may use hybridization or amplification technology tocompare gene expression in a biological sample from a patient tostandard samples in order to detect altered gene expression. Qualitativeor quantitative methods for this comparison are well known in the art.

[0098] For example, the cDNA may be labeled by standard methods andadded to a biological sample from a patient under conditions forhybridization complex formation. After an incubation period, the sampleis washed and the amount of label (or signal) associated withhybridization complexes is quantified and compared with a standardvalue. If the amount of label in the patient sample is significantlyaltered in comparison to the standard value, then the presence of theassociated condition, disease or disorder is indicated.

[0099] In order to provide a basis for the diagnosis of a condition,disease or disorder associated with gene expression, a normal orstandard expression profile is established. This may be accomplished bycombining a biological sample taken from normal subjects, either animalor human, with a probe under conditions for hybridization oramplification. Standard hybridization may be quantified by comparing thevalues obtained using normal subjects with values from an experiment inwhich a known amount of a substantially purified target sequence isused. Standard values obtained in this manner may be compared withvalues obtained from samples from patients who are symptomatic for aparticular condition, disease, or disorder. Deviation from standardvalues toward those associated with a particular condition is used todiagnose that condition.

[0100] Such assays may also be used to evaluate the efficacy of aparticular therapeutic treatment regimen in animal studies and inclinical trial or to monitor the treatment of an individual patient.Once the presence of a condition is established and a treatment protocolis initiated, diagnostic assays may be repeated on a regular basis todetermine if the level of expression in the patient begins toapproximate that which is observed in a normal subject. The resultsobtained from successive assays may be used to show the efficacy oftreatment over a period ranging from several days to months.

[0101] Gene Expression Profiles

[0102] A gene expression profile comprises a plurality of cDNAs and aplurality of detectable hybridization complexes, wherein each complex isformed by hybridization of one or more probes to one or morecomplementary sequences in a sample. The cDNA composition of theinvention is used as elements on a microarray to analyze gene expressionprofiles. In one embodiment, the microarray is used to monitor theprogression of disease. Researchers can assess and catalog thedifferences in gene expression between healthy and diseased tissues orcells. By analyzing changes in patterns of gene expression, disease canbe diagnosed at earlier stages before the patient is symptomatic. Theinvention can be used to formulate a prognosis and to design a treatmentregimen. The invention can also be used to monitor the efficacy oftreatment. For treatments with known side effects, the microarray isemployed to improve the treatment regimen. A dosage is established thatcauses a change in genetic expression patterns indicative of successfultreatment. Expression patterns associated with the onset of undesirableside effects are avoided. This approach may be more sensitive and rapidthan waiting for the patient to show inadequate improvement, or tomanifest side effects, before altering the course of treatment.

[0103] In another embodiment, animal models which mimic a human diseasecan be used to characterize expression profiles associated with aparticular condition, disorder or disease; or treatment of thecondition, disorder or disease. Novel treatment regimens may be testedin these animal models using microarrays to establish and then followexpression profiles over time. In addition, microarrays may be used withcell cultures or tissues removed from animal models to rapidly screenlarge numbers of candidate drug molecules, looking for ones that producean expression profile similar to those of known therapeutic drugs, withthe expectation that molecules with the same expression profile willlikely have similar therapeutic effects. Thus, the invention providesthe means to rapidly determine the molecular mode of action of a drug.

[0104] Assays Using Antibodies

[0105] Antibodies directed against epitopes on a protein encoded by acDNA of the invention may be used in assays to quantify the amount ofprotein found in a particular human cell. Such assays include methodsutilizing the antibody and a label to detect expression level undernormal or disease conditions. The antibodies may be used with or withoutmodification, and labeled by joining them, either covalently ornoncovalently, with a labeling moiety.

[0106] Protocols for detecting and measuring protein expression usingeither polyclonal or monoclonal antibodies are well known in the art.Examples include ELISA, RIA, and fluorescent activated cell sorting(FACS). Such immunoassays typically involve the formation of complexesbetween the protein and its specific antibody and the measurement ofsuch complexes. These and other assays are described in Pound (supra).The method may employ a two-site, monoclonal-based immunoassay utilizingmonoclonal antibodies reactive to two non-interfering epitopes, or acompetitive binding assay. (See, e.g., Coligan et al. (1997) CurrentProtocols in Immunology, Wiley-Interscience, New York N.Y.; Pound,supra)

[0107] Therapeutics

[0108] The cDNAs and fragments thereof can be used in gene therapy.cDNAs can be delivered ex vivo to target cells, such as cells of bonemarrow. Once stable integration and transcription and or translation areconfirmed, the bone marrow may be reintroduced into the subject.Expression of the protein encoded by the cDNA may correct a disorderassociated with mutation of a normal sequence, reduction or loss of anendogenous target protein, or overepression of an endogenous or mutantprotein. Alternatively, cDNAs may be delivered in vivo using vectorssuch as retrovirus, adenovirus, adeno-associated virus, herpes simplexvirus, and bacterial plasmids. Non-viral methods of gene deliveryinclude cationic liposomes, polylysine conjugates, artificial viralenvelopes, and direct injection of DNA (Anderson (1998) Nature392:25-30; Dachs et al. (1997) Oncol Res 9:313-325; Chu et al. (1998) JMol Med 76(34):184Weiss et al. (1999) Cell Mol Life Sci 55(3):334-358;Agrawal (1996) Antisense Therapeutics, Humana Press, Totowa N.J.; andAugust et al. (1997) Gene Therapy (Advances in Pharmacology. Vol. 40),Academic Press, San Diego Calif.).

[0109] In addition, expression of a particular protein can be regulatedthrough the specific binding of a fragment of a cDNA to a genomicsequence or an mRNA which encodes the protein or directs itstranscription or translation. The cDNA can be modified or derivatized toany RNA-like or DNA-like material including peptide nucleic acids,branched nucleic acids, and the like. These sequences can be producedbiologically by transforming an appropriate host cell with a vectorcontaining the sequence of interest.

[0110] Molecules which regulate the activity of the cDNA or encodedprotein are useful as therapeutics for hyperlipidemia. Such moleculesinclude agonists which increase the expression or activity of thepolynucleotide or encoded protein, respectively; or antagonists whichdecrease expression or activity of the polynucleotide or encodedprotein, respectively. In one aspect, an antibody which specificallybinds the protein may be used directly as an antagonist or indirectly asa delivery mechanism for bringing a pharmaceutical agent to cells ortissues which express the protein.

[0111] Additionally, any of the proteins, or their ligands, orcomplementary nucleic acid sequences may be administered aspharmaceutical compositions or in combination with other appropriatetherapeutic agents. Selection of the appropriate agents for use incombination therapy may be made by one of ordinary skill in the art,according to conventional pharmaceutical principles. The combination oftherapeutic agents may act synergistically to affect the treatment orprevention of the conditions and disorders associated with an immuneresponse. Using this approach, one may be able to achieve therapeuticefficacy with lower dosages of each agent, thus reducing the potentialfor adverse side effects. Further, the therapeutic agents may becombined with pharmaceutically-acceptable carriers including excipientsand auxiliaries which facilitate processing of the active compounds intopreparations which can be used pharmaceutically. Further details ontechniques for formulation and administration used by doctors andpharmacists may be found in the latest edition of Remington'sPharmaceutical Sciences (Maack Publishing, Easton Pa.).

[0112] Model Systems

[0113] Animal models may be used as bioassays where they exhibit aphenotypic response similar to that of humans and where exposureconditions are relevant to human exposures. Mammals are the most commonmodels, and most infectious agent, cancer, drug, and toxicity studiesare performed on rodents such as rats or mice because of low cost,availability, lifespan, reproductive potential, and abundant referenceliterature. Inbred and outbred rodent strains provide a convenient modelfor investigation of the physiological consequences of underexpressionor overexpression of genes of interest and for the development ofmethods for diagnosis and treatment of diseases. A mammal inbred tooverexpress a particular gene (for example, secreted in milk) may alsoserve as a convenient source of the protein expressed by that gene.

[0114] Transgenic Animal Models

[0115] Transgenic rodents that overexpress or underexpress a gene ofinterest may be inbred and used to model human diseases or to testtherapeutic or toxic agents. (See, e.g., U.S. Pat. No. 5,175,383 andU.S. Pat. No. 5,767,337.) In some cases, the introduced gene may beactivated at a specific time in a specific tissue type during fetal orpostnatal development. Expression of the transgene is monitored byanalysis of phenotype, of tissue-specific mRNA expression, or of serumand tissue protein levels in transgenic animals before, during, andafter challenge with experimental drug therapies.

[0116] Embryonic Stem Cells

[0117] Embryonic (ES) stem cells isolated from rodent embryos retain thepotential to form embryonic tissues. When ES cells such as the mouse129/SvJ cell line are placed in a blastocyst from the C57BL/6 mousestrain, they resume normal development and contribute to tissues of thelive-born animal. ES cells are preferred for use in the creation ofexperimental knockout and knockin animals. The method for this processis well known in the art and the steps are: the cDNA is introduced intoa vector, the vector is transformed into ES cells, transformed cells areidentified and microinjected into mouse cell blastocysts, blastocystsare surgically transferred to pseudopregnant dams. The resultingchimeric progeny are genotyped and bred to produce heterozygous orhomozygous strains.

[0118] Knockout Analysis

[0119] In gene knockout analysis, a region of a gene is enzymaticallymodified to include a non-natural intervening sequence such as theneomycin phosphotransferase gene (neo; Capecchi (1989) Science244:1288-1292). The modified gene is transformed into cultured ES cellsand integrates into the endogenous genome by homologous recombination.The inserted sequence disrupts transcription and translation of theendogenous gene.

[0120] Knockin Analysis

[0121] ES cells can be used to create knockin humanized animals ortransgenic animal models of human diseases. With knockin technology, aregion of a human gene is injected into animal ES cells, and the humansequence integrates into the animal cell genome. Transgenic progeny orinbred lines are studied and treated with potential pharmaceuticalagents to obtain information on the progression and treatment of theanalogous human condition.

[0122] As described herein, the uses of the cDNAs, provided in theSequence Listing of this application, and their encoded proteins areexemplary of known techniques and are not intended to reflect anylimitation on their use in any technique that would be known to theperson of average skill in the art. Furthermore, the cDNAs provided inthis application may be used in molecular biology techniques that havenot yet been developed, provided the new techniques rely on propertiesof nucleotide sequences that are currently known to the person ofordinary skill in the art, e.g., the triplet genetic code, specific basepair interactions, and the like. Likewise, reference to a method mayinclude combining more than one method for obtaining or assembling fulllength cDNA sequences that will be known to those skilled in the art. Itis also to be understood that this invention is not limited to theparticular methodology, protocols, and reagents described, as these mayvary. It is also understood that the terminology used herein is for thepurpose of describing particular embodiments only, and is not intendedto limit the scope of the present invention which will be limited onlyby the appended claims. The examples below are provided to illustratethe subject invention and are not included for the purpose of limitingthe invention.

EXAMPLES

[0123] IConstruction of cDNA Libraries

[0124] RNA was purchased from Clontech Laboratories (Palo Alto Calif.)or isolated from various tissues. Some tissues were homogenized andlysed in guanidinium isothiocyanate, while others were homogenized andlysed in phenol or in a suitable mixture of denaturants, such as TRIZOLreagent (Life Technologies, Rockville Md.). The resulting lysates werecentrifuged over CsCl cushions or extracted with chloroform. RNA wasprecipitated with either isopropanol or ethanol and sodium acetate, orby other routine methods.

[0125] Phenol extraction and precipitation of RNA were repeated asnecessary to increase RNA purity. In most cases, RNA was treated withDNase. For most libraries, poly(A) RNA was isolated using oligod(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles(Qiagen, Valencia Calif.), or an OLIGOTEX mRNA purification kit(Qiagen). Alternatively, poly(A) RNA was isolated directly from tissuelysates using other kits, including the POLY(A)PURE mRNA purificationkit (Ambion, Austin Tex.).

[0126] In some cases, Stratagene (La Jolla Calif.) was provided with RNAand constructed the corresponding cDNA libraries. Otherwise, cDNA wassynthesized and cDNA libraries were constructed with the UNIZAP vectorsystem (Stratagene) or SUPERSCRIPT plasmid system (Life Technologies)using the recommended procedures or similar methods known in the art.(See Ausubel, supra, Units 5.1 through 6.6.) Reverse transcription wasinitiated using oligo d(T) or random primers. Synthetic oligonucleotideadapters were ligated to double stranded cDNA, and the cDNA was digestedwith the appropriate restriction enzyme or enzymes. For most libraries,the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000,SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (APB) orpreparative agarose gel electrophoresis. cDNAs were ligated intocompatible restriction enzyme sites of the polylinker of the PBLUESCRIPTphagemid (Stratagene), PSPORT1 plasmid (Life Technologies), or PINCYplasmid (Incyte Genomics). Recombinant plasmids were transformed intoXL1-BLUE, XL1-BLUEMRF, or SOLR competent E. coli cells (Stratagene) orDH5a, DH10B, or ELECTROMAX DH10B competent E. coli cells (LifeTechnologies).

[0127] In some cases, libraries were superinfected with a 5×excess ofthe helper phage, M13K07, according to the method of Vieira et al.(1987, Methods Enzymol. 153:3-11) and normalized or subtracted using amethodology adapted from Soares (1994, Proc Natl Acad Sci 91:9228-9232),Swaroop et al. (1991, Nucl Acids Res 19:1954), and Bonaldo et al. (1996,Genome Research 6:791-806). The modified Soares normalization procedurewas utilized to reduce the repetitive cloning of highly expressed highabundance cDNAs while maintaining the overall sequence complexity of thelibrary. Modification included significantly longer hybridization timeswhich allowed for increased gene discovery rates by biasing thenormalized libraries toward those infrequently expressed low-abundancecDNAs which are poorly represented in a standard transcript image(Soares et al., supra).

[0128] II Isolation and Sequencing of cDNA Clones

[0129] Plasmids were recovered from host cells by in vivo excision usingthe UNIZAP vector system (Stratagene) or by cell lysis. Plasmids werepurified using one of the following: the Magic or WIZARD MINIPREPS DNApurification system (Promega); the AGTC MINIPREP purification kit (EdgeBioSystems, Gaithersburg Md.); the QIAWELL 8, QIAWELL 8 Plus, or QIAWELL8 Ultra plasmid purification systems, or the REAL PREP 96 plasmidpurification kit (QIAGEN). Following precipitation, plasmids wereresuspended in 0.1 ml of distilled water and stored, with or withoutlyophilization, at 4° C.

[0130] Alternatively, plasmid DNA was amplified from host cell lysatesusing direct link PCR in a high-throughput format (Rao (1994) AnalBiochem 216:1-14). Host cell lysis and thermal cycling steps werecarried out in a single reaction mixture. Samples were processed andstored in 384-well plates, and the concentration of amplified plasrnidDNA was quantified fluorometrically using PICOGREEN dye (MolecularProbes) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy,Helsinki, Finland).

[0131] cDNA sequencing reactions were processed using standard methodsor high-throughput instrumentation such as the ABI CATALYST 800 thermalcycler (Applied Biosystems) or the DNA ENGINE thermal cycler (MJResearch, Watertown Mass.) in conjunction with the HYDRA microdispenser(Robbins Scientific, Sunnyvale Calif.) or the MICROLAB 2200 system(Hamilton, Reno Nev.). cDNA sequencing reactions were prepared usingreagents provided by APB or supplied in ABI sequencing kits such as theABI PRISM BIGDYE cycle sequencing kit (Applied Biosystems).Electrophoretic separation of cDNA sequencing reactions and detection oflabeled cDNAs were carried out using the MEGABACE 1000 DNA sequencingsystem (APB); the ABI PRISM 373 or 377 sequencing systems (AppliedBiosystems) in conjunction with standard ABI protocols and base callingsoftware; or other sequence analysis systems known in the art. Readingframes within the cDNA sequences were identified using standard methods(reviewed in Ausubel, supra, Unit 7.7).

[0132] III Extension of cDNA Sequences

[0133] Nucleic acid sequences were extended using the cDNA clones andoligonucleotide primers. One primer was synthesized to initiate 5′extension of the known fragment, and the other, to initiate 3′ extensionof the known fragment. The initial primers were designed using OLIGO4.06 software (National Biosciences), or another appropriate program, tobe about 22 to 30 nucleotides in length, to have a GC content of about50% or more, and to anneal to the target sequence at temperatures ofabout 68° C. to about 72° C. Any stretch of nucleotides which wouldresult in hairpin structures and primer-primer dimerizations wasavoided.

[0134] Selected human cDNA libraries were used to extend the sequence.If more than one extension was necessary or desired, additional ornested sets of primers were designed. Preferred libraries are ones thathave been size-selected to include larger cDNAs. Also, random primedlibraries are preferred because they will contain more sequences withthe 5′ and upstream regions of genes. A randomly primed library isparticularly useful if an oligo d(T) library does not yield afull-length cDNA.

[0135] High fidelity amplification was obtained by PCR using methodswell known in the art. PCR was performed in 96-well plates using the DNAENGINE thermal cycler (MJ Research). The reaction mix contained DNAtemplate, 200 nmol of each primer, reaction buffer containing Mg² ⁺,(NH₄)₂SO₄, and β-mercaptoethanol, Taq DNA polymerase (APB), ELONGASEenzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), withthe following parameters for primer pair PCI A and PCI B (IncyteGenomics): Step 1: 94° C., 3 min; Step 2:94° C., 15 sec; Step 3:60° C.,1 min; Step 4:68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20times; Step 6:68° C., 5 min; Step 7: storage at 4° C. In thealternative, the parameters for primer pair T7 and SK+(Stratagene) wereas follows: Step 1:94° C., 3 min; Step 2:94° C., 15 sec; Step 3:57° C.,1 min; Step 4:68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C.

[0136] The concentration of DNA in each well was determined bydispensing 100 μl PICOGREEN reagent (0.25% reagent in 1×x TE, v/v;Molecular Probes) and 0.5 μl of undiluted PCR product into each well ofan opaque fluorimeter plate (Corning Costar, Acton Mass.) and allowingthe DNA to bind to the reagent. The plate was scanned in a FLUOROSKAN II(Labsystems Oy) to measure the fluorescence of the sample and toquantify the concentration of DNA. A 5,μl to 10 μl aliquot of thereaction mixture was analyzed by electrophoresis on a 1% agarosemini-gel to determine which reactions were successful in extending thesequence.

[0137] The extended nucleic acids were desalted and concentrated,transferred to 384-well plates, digested with CviJI cholera virusendonuclease (Molecular Biology Research, Madison Wis.), and sonicatedor sheared prior to religation into pUC18 vector (APB). For shotgunsequencing, the digested nucleic acids were separated on lowconcentration (0.6 to 0.8%) agarose gels, fragments were excised, andagar digested with AGARACE enzyme (Promega). Extended clones werereligated using T4 DNA ligase (New England Biolabs, Beverly Mass.) intopUC18 vector (APB), treated with Pfu DNA polymerase (Stratagene) tofill-in restriction site overhangs, and transformed into competent E.coli cells. Transformed cells were selected on antibiotic-containingmedia, and individual colonies were picked and cultured overnight at 37°C. in 384-well plates in LB/2×carbenicillin liquid media.

[0138] The cells were lysed, and DNA was amplified by PCR using Taq DNApolymerase (APB) and Pfu DNA polymerase (Stratagene) with the followingparameters: Step 1:94° C., 3 min; Step 2:94° C., 15 sec; Step 60° C., 1min; Step 4:72° C., 2 min; Step 5: steps 2, 3, and 4 repeated 29 times;Step storage at 4° C. DNA was quantified using PICOGREEN reagent(Molecular Probes) as described above. Samples with low DNA recoverieswere reamplified using the same conditions described above. Samples werediluted with 20% dimethylsulfoxide (DMSO; 1:2, v/v), and sequenced usingDYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECTcycle sequencing kit (APB) or the ABI PRISM BIGDYE terminator cyclesequencing kit (Applied Biosystems).

[0139] IV Assembly and Analysis of Sequences

[0140] Component nucleotide sequences from chromatograms were subjectedto PHRED analysis (Phil Green, University of Washington, Seattle Wash.)and assigned a quality score. The sequences having at least a requiredquality score were subject to various pre-processing algorithms toeliminate low quality 3′ ends, vector and linker sequences, polyA tails,Alu repeats, mitochondrial and ribosomal sequences, bacterialcontamination sequences, and sequences smaller than 50 base pairs.Sequences were screened using the BLOCK 2 program (Incyte Genomics), amotif analysis program based on sequence information contained in theSWISS-PROT and PROSRIT databases (Bairoch et al. (1997) Nucleic AcidsRes 25:217-221; Attwood et al. (1997) J Chem Inf Comput Sci 37:417-424).

[0141] Processed sequences were subjected to assembly procedures inwhich the sequences were assigned to bins, one sequence per bin.Sequences in each bin were assembled to produce consensus sequences,templates. Subsequent new sequences were added to existing bins usingBLAST (Altschul (supra); Altschul et al. (supra); Karlin et al. (1988)Proc Natl Acad Sci 85-841-845), BLASTn (vers. 1.4, WashU), andCROSSMATCH software (Phil Green, supra). Candidate pairs were identifiedas all BLAST hits having a quality score greater than or equal to 150.Alignments of at least 82% local identity were accepted into the bin.The component sequences from each bin were assembled using PHRAP (PhilGreen, supra). Bins with several overlapping component sequences wereassembled using DEEP PHRAP (Phil Green, supra).

[0142] Bins were compared against each other, and those having localsimilarity of at least 82% were combined and reassembled. Reassembledbins having templates of insufficient overlap (less than 95% localidentity) were re-split. Assembled templates were also subjected toanalysis by STITCHER/EXON MAPPER algorithms which analyzed theprobabilities of the presence of splice variants, alternatively splicedexons, splice junctions, differential expression of alternative splicedgenes across tissue types, disease states, and the like. These resultingbins were subjected to several rounds of the above assembly proceduresto generate the template sequences found in the LIFESEQ GOLD database(Incyte Genomics).

[0143] The assembled templates were annotated using the followingprocedure. Template sequences were analyzed using BLASTn (vers. 2.0,NCBI) versus GBpri (GenBank vers. 116). “Hits” were defined as an exactmatch having from 95% local identity over 200 base pairs through 100%local identity over 100 base pairs, or a homolog match having an E-valueequal to or greater than 1×10⁻⁸. (The “E-value” quantifies thestatistical probability that a match between two sequences occurred bychance). The hits were subjected to frameshift FAST×versus GENPEPT(GenBank version 109). In this analysis, a homolog match was defined ashaving an E-value of 1×10 ⁻⁸. The assembly method used above wasdescribed in U.S. Ser. No. 09/276,534, filed Mar. 25, 1999, and theLIFESEQ GOLD user manual (Incyte Genomics).

[0144] Following assembly, template sequences were subjected to motif,BLAST, Hidden Markov Model (HMM; Pearson and Lipman (1988) Proc NatlAcad Sci 85:2444-2448; Smith and Waterman (1981) J Mol Biol147:195-197), and functional analyses, and categorized in proteinhierarchies using methods described in U.S. Ser. No. 08/812,290, filedMar. 6, 1997; U.S. Ser. No. 08/947,845, filed Oct. 9, 1997; U.S. Pat.No. 5,953,727; and U.S. Ser. No. 09/034,807, filed Mar.4, 1998. Templatesequences may be further queried against public databases such as theGenBank rodent, mammalian, vertebrate, eukaryote, prokaryote, and humanEST databases.

[0145] V Selection of Sequences, Microarray Preparation and Use p Incyteclones represent template sequences derived from the LIFESEQ GOLDassembled human sequence database (Incyte Genomics). In cases where morethan one clone was available for a particular template, the 5′-mostclone in the template was used on the microarray. The GENEALBUM GEMseries 1-6 microarrays (Incyte Genomics) contain 52,616 array elementswhich represent 17,472 annotated clusters and 35,144 unannotatedclusters. The HUMAN GENOME GEM series 1-3 microarrays (Incyte Genomics)contain 28,626 array elements which represent 10,068 annotated clustersand 18,558 unannotated clusters. For the UNIGEM series microarrays(Incyte Genomics), Incyte clones were mapped to non-redundant Unigeneclusters (Unigene database (build 46), NCBI; Shuler (1997) J Mol Med75:694-698), and the 5′ clone with the strongest BLAST alignment (atleast 90% identity and 100 bp overlap) was chosen, verified, and used inthe construction of the microarray. The UNIGEM V microarray (IncyteGenomics) contains 7075 array elements which represent 4610 annotatedgenes and 2,184 unannotated clusters. Table 3 shows the GenBankannotations for SEQ ID NOs: 1-401 of this invention as produced by BLASTanalysis.

[0146] To construct microarrays, cDNAs were amplified from bacterialcells using primers complementary to vector sequences flanking the cDNAinsert. Thirty cycles of PCR increased the initial quantity of cDNAsfrom 1-2 ng to a final quantity greater than 5 μg. Amplified cDNAs werethen purified using SEPHACRYL-400 columns (APB). Purified cDNAs wereimmobilized on polymer-coated glass slides. Glass microscope slides(Corning, Corning N.Y.) were cleaned by ultrasound in 0.1% SDS andacetone, with extensive distilled water washes between and aftertreatments. Glass slides were etched in 4% hydrofluoric acid (VWRScientific Products, West Chester Pa.), washed thoroughly in distilledwater, and coated with 0.05% aminopropyl silane (Sigma Aldrich) in 95%ethanol. Coated slides were cured in a 110° C. oven. cDNAs were appliedto the coated glass substrate using a procedure described in U.S. Pat.No. 5,807,522. One microliter of the cDNA at an average concentration of100 ng/ul was loaded into the open capillary printing element by ahigh-speed robotic apparatus which then deposited about 5 nl of cDNA perslide.

[0147] Microarrays were UV-crosslinked using a STRATALINKERUV-crosslinker (Stratagene), and then washed at room temperature once in0.2% SDS and three times in distilled water. Non-specific binding siteswere blocked by incubation of microarrays in 0.2% casein in phosphatebuffered saline (Tropix, Bedford Mass.) for 30 minutes at 60° C.followed by washes in 0.2% SDS and distilled water as before.

[0148] VI Preparation of Samples

[0149] Treatment of human C3A cell cultures

[0150] Early confluent C3A cells (ATTC, Manassas Va.) were treated withcaptopril (0.5, 2, 48, and 60 μg/ml) for 1, 3, and 6 hours. Earlyconfluent C3A cells were treated with enalapril (0.5, 2, 48, and 60μg/ml) for 1, 3, and 6 hours. Early confluent C3A cells were treatedwith LY294002 (0.5, 2, 15, and 25 μg/ml) for 1, 3, and 6 hours. Earlyconfluent C3A cells were starved of insulin for 3 days prior totreatment, then treated with LY294002 (10 μM) for 2, 24, 36, and 72hours in the presence of insulin. Early confluent C3A cells were treatedwith DES (1, 10, and 100 μM) for 1, 3, and 6 hours. Early confluent C3Acells were treated with dexamethasone (1 and 20 μM) for 0, 2, 6, and 24hours. Early confluent C3A cells were treated with MCA (0.5 and 10 μM)for 2, 6, and 24 hours. In all cases mRNA from untreated early confluentcells were prepared in parallel as described below.

[0151] Isolation and Labeling of Sample cDNAs

[0152] Cells were harvested and lysed in 1 ml of TRIZOL reagent (5×10⁶cells/ml; Life Technologies). The lysates were vortexed thoroughly andincubated at room temperature for 2-3 minutes and extracted with 0.5 mlchloroform. The extract was mixed, incubated at room temperature for 5minutes, and centrifuged at 15,000 rpm for 15 minutes at 4° C. Theaqueous layer was collected and an equal volume of isopropanol wasadded. Samples were mixed, incubated at room temperature for 10 minutes,and centrifuged at 15,000 rpm for 20 minutes at 4° C. The supernatantwas removed and the RNA pellet was washed with 1 ml of 70% ethanol,centrifuged at 15,000 rpm at 4° C., and resuspended in RNase-free water.The concentration of the RNA was determined by measuring the opticaldensity at 260 nm.

[0153] Poly(A) RNA was prepared using an OLIGOTEX mRNA kit (QIAGEN) withthe following modifications: OLIGOTEX beads were washed in tubes insteadof on spin columns, resuspended in elution buffer, and then loaded ontospin columns to recover mRNA. To obtain maximum yield, the mRNA waseluted twice.

[0154] Each poly(A) RNA sample was reverse transcribed using MMLVreverse-transcriptase, 0.05 pg/μl oligo-d(T) primer (21mer), 1×firststrand buffer, 0.03 units/ul RNase inhibitor, 500 uM dATP, 500 uM dGTP,500 uM dTTP, 40 uM dCTP, and 40 uM either dCTP-Cy3 or dCTP-Cy5 (APB).The reverse transcription reaction was performed in a 25 mnl volumecontaining 200 ng poly(A) RNA using the GEMBRIGHT kit (Incyte Genomics).Specific control poly(A) RNAs (YCFR06, YCFR45, YCFR67, YCFR85, YCFR43,YCFR22, YCFR23, YCFR25, YCFR44, YCFR26) were synthesized by in vitrotranscription from non-coding yeast genomic DNA (W. Lei, unpublished).As quantitative controls, control InRNAs (YCFR06, YCFR45, YCFR67, andYCFR85) at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng were diluted into reversetranscription reaction at ratios of 1:100,000, 1:10,000, 1:1000, 1:100(w/w) to sample mRNA, respectively. To sample differential expressionpatterns, control mRNAs (YCFR43, YCFR22, YCFR23, YCFR25, YCFR44, YCFR26)were diluted into reverse transcription reaction at ratios of 1:3, 3:1,1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA. Reactions were incubated at37° C. for 2 hr, treated with 2.5 ml of 0.5M sodium hydroxide, andincubated for 20 minutes at 85° C. to the stop the reaction and degradethe RNA.

[0155] cDNAs were purified using two successive CHROMA SPIN 30 gelfiltration spin columns (Clontech). Cy3- and Cy5-labeled reactionsamples were combined as described below and ethanol precipitated using1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100%ethanol. The cDNAs were then dried to completion using a SpeedVAC system(Savant Instruments, Holbrook N.Y.) and resuspended in 14 μl 5×SSC/0.2%SDS.

[0156] VII Hybridization and Detection

[0157] Hybridization reactions contained 9 μl of sample mixturecontaining 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in5×SSC, 0.2% SDS hybridization buffer. The mixture was heated to 65° C.for 5 minutes and was aliquoted onto the microarray surface and coveredwith an 1.8 cm² coverslip. The microarrays were transferred to awaterproof chamber having a cavity just slightly larger than amicroscope slide. The chamber was kept at 100% humidity internally bythe addition of 140 μl of 5×SSC in a corner of the chamber. The chambercontaining the microarrays was incubated for about 6.5 hours at 60° C.The microarrays were washed for 10 min at 45° C. in low stringency washbuffer (1×SSC, 0.1% SDS), three times for 10 minutes each at 45° C. inhigh stringency wash buffer (0.1×SSC), and dried.

[0158] Reporter-labeled hybridization complexes were detected with amicroscope equipped with an Innova 70 mixed gas 10 W laser (Coherent,Santa Clara Calif.) capable of generating spectral lines at 488 nm forexcitation of Cy3 and at 632 nm for excitation of Cy5. The excitationlaser light was focused on the microarray using a 20×microscopeobjective (Nikon, Melville N.Y.). The slide containing the microarraywas placed on a computer-controlled X-Y stage on the microscope andraster-scanned past the objective. The 1.8 cm×1.8 cm microarray used inthe present example was scanned with a resolution of 20 micrometers.

[0159] In two separate scans, the mixed gas multiline laser excited thetwo fluorophores sequentially. Emitted light was split, based onwavelength, into two photomultiplier tube detectors (PMT R1477;Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the twofluorophores. Appropriate filters positioned between the microarray andthe photomultiplier tubes were used to filter the signals. The emissionmaxima of the fluorophores used were 565 nm for Cy3 and 650 nm for Cy5.Each microarray was typically scanned twice, one scan per fluorophoreusing the appropriate filters at the laser source, although theapparatus was capable of recording the spectra from both fluorophoressimultaneously.

[0160] The sensitivity of the scans was calibrated using the signalintensity generated by a cDNA control species. Samples of thecalibrating cDNA were separately labeled with the two fluorophores andidentical amounts of each were added to the hybridization mixture. Aspecific location on the microarray contained a complementary DNAsequence, allowing the intensity of the signal at that location to becorrelated with a weight ratio of hybridizing species of 1:100,000.

[0161] The output of the photomultiplier tube was digitized using a12-bit RTI-835H analog-to-digital (A/D) conversion board (AnalogDevices, Norwood, Ma.) installed in an IBM-compatible PC computer. Thedigitized data were displayed as an image where the signal intensity wasmapped using a linear 20-color transformation to a pseudocolor scaleranging from blue (low signal) to red (high signal). The data was alsoanalyzed quantitatively. Where two different fluorophores were excitedand measured simultaneously, the data were first corrected for opticalcrosstalk (due to overlapping emission spectra) between the fluorophoresusing each fluorophore's emission spectrum.

[0162] A grid was superimposed over the fluorescence signal image suchthat the signal from each spot was centered in each element of the grid.The fluorescence signal within each element was then integrated toobtain a numerical value corresponding to the average intensity of thesignal. The software used for signal analysis was the GEMTOOLS geneexpression analysis program (Incyte Genornics). Significance was definedas signal to background ratio exceeding 2×and area hybridizationexceeding 40%.

[0163] VIII Data Analysis and Results

[0164] Array elements that exhibited at least 2-fold change inexpression at one or more time points, a signal intensity over 250units, a signal-to-background ratio of at least 2.5, and an element spotsize of at least 40% were identified as differentially expressed usingthe GEMTOOLS program (Incyte Genomics). The cDNAs that aredifferentially expressed are shown in Table 1. Table I identifiesupregulated and downregulated cDNAs. The cDNAs are further identified bytheir SEQ ID NO and TEMPLATE ID, and by the description associated withat least a fragment of a polynucleotide found in GenBank as shown inTables 2 and 3. The descriptions were obtained using the sequences ofthe Sequence Listing and BLAST analysis.

[0165] IX Other Hybridization Technologies and Analyses

[0166] Other hybridization technologies utilize a variety of substratessuch as nylon membranes, capillary tubes, etc. Arranging cDNAs onpolymer coated slides is described in Example V; sample cDNA preparationand hybridization and analysis using polymer coated slides is describedin examples VI and VII, respectively.

[0167] The cDNAs are applied to a membrane substrate by one of thefollowing methods. A mixture of cDNAs is fractionated by gelelectrophoresis and transferred to a nylon membrane by capillarytransfer. Alternatively, the cDNAs are individually ligated to a vectorand inserted into bacterial host cells to form a library. The cDNAs arethen arranged on a substrate by one of the following methods. In thefirst method, bacterial cells containing individual clones arerobotically picked and arranged on a nylon membrane. The membrane isplaced on LB agar containing selective agent (carbenicillin, kanamycin,ampicillin, or chloramphenicol depending on the vector used) andincubated at 37° C. for 16 hr. The membrane is removed from the agar andconsecutively placed colony side up in 10% SDS, denaturing solution (1.5M NaCl, 0.5 M NaOH ), neutralizing solution (1.5 M NaCl, 1 M Tris, pH8.0), and twice in 2×SSC for 10 min each. The membrane is then LTVirradiated in a STRATALINKER UV-crosslinker (Stratagene).

[0168] In the second method, cDNAs are amplified from bacterial vectorsby thirty cycles of PCR using primers complementary to vector sequencesflanking the insert. PCR amplification increases a startingconcentration of 1-2 ng nucleic acid to a final quantity greater than 5μg. Amplified nucleic acids from about 400 bp to about 5000 bp in lengthare purified using SEPHACRYL-400 beads (APB). Purified nucleic acids arearranged on a nylon membrane manually or using a dot/slot blottingmanifold and suction device and are immobilized by denaturation,neutralization, and LTV irradiation as described above.

[0169] Hybridization probes derived from cDNAs of the Sequence Listingare employed for screening cDNAs, mRNAs, or genomic DNA inmembrane-based hybridizations. Probes are prepared by diluting the cDNAsto a concentration of 40-50 ng in 45 μl TE buffer, denaturing by heatingto 100° C. for five min and briefly centrifuging. The denatured cDNA isthen added to a REDIPRIME tube (APB), gently mixed until blue color isevenly distributed, and briefly centrifuged. Five microliters of[³²P]dCTP is added to the tube, and the contents are incubated at 37° C.for 10 min. The labeling reaction is stopped by adding 5 μl of 0.2MEDTA, and probe is purified from unincorporated nucleotides using aPROBEQUANT G-50 microcolumn (APB). The purified probe is heated to 100°C. for five min and then snap cooled for two min on ice. Membranes arepre-hybridized in hybridization solution containing 1% Sarkosyl and1×high phosphate buffer (0.5 M NaCl, 0.1 M Na₂HP O₄, 5 mM EDTA, pH 7) at55° C. for two hr. The probe, dilut fresh hybridization solution, isthen added to the membrane. The membrane is hybridized with the probe at55° C. for 16 hr. Following hybridization, the membrane is washed for 15min at 25° C. in 1 mM Tris (pH 8.0), 1% Sarkosyl, and four times for 15min each at 25° C. in 1 mM Tris (pH 8.0). To detect hybridizationcomplexes, XOMAT-AR film (Eastman Kodak, Rochester N.Y.) is exposed tothe membrane overnight at −70° C., developed, and examined.

[0170] X Further Characterization of Differentially Expressed cDNAs andProteins

[0171] Clones were blasted against the LIFESEQ Gold 5.1 database (IncyteGenomics) and an Incyte template and its sequence variants were chosenfor each clone. The template and variant sequences were blasted againstGenBank database to acquire annotation. The nucleotide sequences weretranslated into amino acid sequence which was blasted against theGenPept and other protein databases to acquire annotation andcharacterization, i.e., structural motifs.

[0172] Percent sequence identity can be determined electronically fortwo or more amino acid or nucleic acid sequences using the MEGALIGNprogram (DNASTAR). The percent identity between two amino acid sequencesis calculated by dividing the length of sequence A, minus the number ofgap residues in sequence A, minus the number of gap residues in sequenceB, into the sum of the residue matches between sequence A and sequenceB, times one hundred. Gaps of low or of no homology between the twoamino acid sequences are not included in determining percentageidentity.

[0173] Sequences with conserved protein motifs may be searched using theBLOCKS search program. This program analyses sequence informationcontained in the Swiss-Prot and PROSITE databases and is useful fordetermining the classification of uncharacterized proteins translatedfrom genomic or cDNA sequences (Bairoch et al.(supra); Attwood et al.(supra). PROSITE database is a useful source for identifying functionalor structural domains that are not detected using motifs due to extremesequence divergence. Using weight matrices, these domains are calibratedagainst the SWISS-PROT database to obtain a measure of the chancedistribution of the matches.

[0174] The PRINTS database can be searched using the BLIMPS searchprogram to obtain protein family “fingerprints”. The PRINTS databasecomplements the PROSITE database by exploiting groups of aconservedmotifs within sequence alignments to build characteristic signatures ofdifferent protein families. For both BLOCKS and PRINTS analyses, thecutoff scores for local similarity were: >1300=strong,1000-1300=suggestive; for global similarity were: p<exp-3; and forstrength (degree of correlation) were: >1300=strong, 1000-1300=weak.

[0175] X Expression of the Encoded Protein

[0176] Expression and purification of a protein encoded by a cDNA of theinvention is achieved using bacterial or virus-based expression systems.For expression in bacteria, cDNA is subcloned into a vector containingan antibiotic resistance gene and an inducible promoter that directshigh levels of cDNA transcription. Examples of such promoters include,but are not limited to, the trp-lac (tac) hybrid promoter and the T5 orT7 bacteriophage promoter in conjunction with the lac operatorregulatory element. Recombinant vectors are transformed into bacterialhosts, such as BL21(DE3). Antibiotic resistant bacteria express theprotein upon induction with IPTG. Expression in eukaryotic cells isachieved by infecting Spodontera frugiperda (Sf9) insect cells withrecombinant baculovirus, Autographica californica nuclear polyhedrosisvirus. The polyhedrin gene of baculovirus is replaced with the cDNA byeither homologous recombination or bacterial-mediated transpositioninvolving transfer plasmid intermediates. Viral infectivity ismaintained and the strong polyhedrin promoter drives high levels oftranscription.

[0177] For ease of purification, the protein is synthesized as a fusionprotein with glutathione-S-transferase (GST; APB) or a similaralternative such as FLAG. The fusion protein is purified on immobilizedglutathione under conditions that maintain protein activity andantigenicity. After purification, the GST moiety is proteolyticallycleaved from the protein with thrombin. A fusion protein with FLAG, an8-amino amino acid peptide, is purified using commercially availablemonoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak, RochesterN.Y.).

[0178] XI Production of Specific Antibodies

[0179] A denatured protein from a reverse phase HPLC separation isobtained in quantities up to 75 mg. This denatured protein is used toimmunize mice or rabbits following standard protocols. About 100 μg isused to immunize a mouse, while up to 1 mg is used to immunize a rabbit.The denatured protein is radioiodinated and incubated with murine B-cellhybridomas to screen for monoclonal antibodies. About 20 mg of proteinis sufficient for labeling and screening several thousand clones.

[0180] In another approach, the amino acid sequence translated from acDNA of the invention is analyzed using PROTEAN software (DNASTAR) todetermine regions of high antigenicity, essentiallyantigenically-effective epitopes of the protein. The optimal sequencesfor immunization are usually at the C-terminus, the N-terminus, andthose intervening, hydrophilic regions of the protein that are likely tobe exposed to the external environment when the protein is in itsnatural conformation. Typically, oligopeptides about 15 residues inlength are synthesized using an ABI 431 Peptide synthesizer (AppliedBiosystems) using Fmoc-chemistry and then coupled to keyhole limpethemocyanin (KLH; Sigma Aldrich) by reaction withM-maleimidobenzoyl-N-hydroxysuccinimide ester. If necessary, a cysteinemay be introduced at the N-termninus of the peptide to permit couplingto KLH. Rabbits are immunized with the oligopeptide-KLH complex incomplete Freund's adjuvant. The resulting antisera are tested forantipeptide activity by binding the peptide to plastic, blocking with 1%BSA, reacting with rabbit antisera, washing, and reacting withradioiodinated goat anti-rabbit IgG.

[0181] Hybridomas are prepared and screened using standard techniques.Hybridomas of interest are detected by screening with radioiodinatedprotein to identify those fusions producing a monoclonal antibodyspecific for the protein. In a typical protocol, wells of 96 well plates(FAST, Becton-Dickinson, Palo Alto Calif.) are coated withaffinity-purified, specific rabbit-anti-mouse (or suitable anti-speciesIg) antibodies at 10 mg/ml. The coated wells are blocked with 1% BSA andwashed and exposed to supernatants from hybridomas. After incubation,the wells are exposed to radiolabeled protein at 1 mg/ml. Clonesproducing antibodies bind a quantity of labeled protein that isdetectable above background.

[0182] Such clones are expanded and subjected to 2 cycles of cloning at1 cell/3 wells. Cloned hybridomas are injected into pristane-treatedmice to produce ascites, and monoclonal antibody is purified from theascitic fluid by affinity chromatography on protein A (APB). Monoclonalantibodies with affinities of at least 10⁸ M⁻¹, preferably 10⁹ to 10¹⁰M⁻¹ or stronger, are made by procedures well known in the art.

[0183] XII Purification of Naturally Occurring Protein Using SpecificAntibodies

[0184] Naturally occurring or recombinant protein is substantiallypurified by immunoaffinity chromatography using antibodies specific forthe protein. An immunoaffinity column is constructed by covalentlycoupling the antibody to CNBr-activated SEPHAROSE resin (APB). Mediacontaining the protein is passed over the immunoaffinity column, and thecolumn is washed using high ionic strength buffers in the presence ofdetergent to allow preferential absorbance of the protein. Aftercoupling, the protein is eluted from the column using a buffer of pH 2-3or a high concentration of urea or thiocyanate ion to disruptantibody/protein binding, and the protein is collected.

[0185] XIII Screening Molecules for Specific Binding with the cDNA orProtein

[0186] The cDNA or fragments thereof and the protein or portions thereofare labeled with ³²P-dCTP, Cy3-dCTP, Cy5-dCTP (APB), or BIODIPY or FITC(Molecular Probes), respectively. Candidate molecules or compoundspreviously arranged on a substrate are incubated in the presence oflabeled nucleic or amino acid. After incubation under conditions foreither a cDNA or a protein, the substrate is washed, and any position onthe substrate retaining label, which indicates specific binding orcomplex formation, is assayed. The binding molecule is identified by itsarrayed position on the substrate. Data obtained using differentconcentrations of the nucleic acid or protein are used to calculateaffinity between the labeled nucleic acid or protein and the boundmolecule. High throughput screening using very small assay volumes andvery small amounts of test compound is fully described in Burbaum et al.U.S. Pat. No. 5,876,946.

[0187] All patents and publications mentioned in the specification areincorporated herein by reference. Various modifications and variationsof the described method and system of the invention will be apparent tothose skilled in the art without departing from the scope and spirit ofthe invention. Although the invention has been described in connectionwith specific preferred embodiments, it should be understood that theinvention as claimed should not be unduly limited to such specificembodiments. Indeed, various modifications of the described modes forcarrying out the invention that are obvious to those skilled in thefield of molecular biology or related fields are intended to be withinthe scope of the following claims. TABLE 1 Clone ID ClofibrateFenofibrate Captopril Enalapril Dexamethasone DES MCA LY294002Ins/LY294002 26474 −4.2 60123 2.6 63038 −3.95 −2.9 −3.16 −2.97 −2.3672713 3 85606 2.96 86390 −2.83 118501 4.87 4.36 6.06 2.79 4.54 −2.4121785 3.3 136073 3.1 160822 2.5 2.39 167081 2.14 172023 −5.8 2.85 −3.38211389 −2.52 237027 −2.85 293477 2.83 271299 2.91 279249 −2.15 2798984.08 5.48 6.7 280932 −2.8 −2.67 293477 2 311346 4.59 318486 4.11 341884−2.32 −3.33 348143 2.11 388964 2.77 389362 2.88 407032 −3.05 408886 4.93419492 2.47 437481 2.44 2.24 442723 2.51 443991 2.47 2.62 450856 2.492.89 452321 3 4.3 454839 3.4 459372 4.65 2.63 460779 2.26 462069 2.41480791 −2.27 481402 3.22 510056 2.73 5.65 511448 3.05 560115 −2.61604019 3.28 630625 2.53 3.95 2.81 2.51 2.52 2.25 669498 −2.97 7014842.51 758192 3.11 773154 −2.39 818192 2.87 872017 2.85 891322 3.81 9635362.93 970905 −4.06 2.25 990375 −2.5 1213932 6.31 1259841 3.15 12724832.51 1306814 2.83 1308112 2.19 2.14 2.28 1315663 −3.18 −4.02 −2.84 −3.271316801 3.38 1326255 −2.7 1368834 2.47 2.43 1379063 −2.38 −4 −2.44 −3.42−3.63 1381654 1.57 2.57 2.64 1395143 3.09 1435374 3.67 1441245 −2.31448718 −2.95 −3.93 −3.91 −3.1 1454436 2.62 1457424 2.93 1457718 2.921464613 −2.39 1468660 −3.3 −2.28 1482116 3.44 1495382 −2.77 1500245 2.921511658 −3.56 1519431 2.36 1519683 −2.12 1522880 2.74 1530595 3.521559665 −4.058 1559756 1.56 2.47 1560906 3.13 1577614 −3.3 1616783 2.552.63 1619292 −3.07 −5 −4.3 −4.4 −2.8 1619980 −2.97 1623214 −2.25 −3.121630990 2.86 3.34 1696224 11.91 3.28 3.97 2.83 4.4 1705208 4.2 2.831711151 2.4 3.05 2.48 1732221 −2.85 1756875 2.99 1786554 2.66 2.671822716 2.45 1833362 −3.7 −2.33 1834236 −2.3 1838114 −2.65 1845046 −2.51846209 1.81 2.2 1846463 3.62 6.58 1861456 −2.51 1867614 5.81 1869130−2.72 1871340 −2.43 1874037 3.63 1874307 −2.57 1890576 −2.5 −3.071890791 2.7 1920215 −2.59 1922468 3.03 1926883 2.94 1930235 2.73 3.25 32.93 1956982 −2.13 1958226 −2.52 1963081 −4.16 1966517 −2.8 1969563 3.786.8 1975268 −2.42 −2.75 −3.35 −2.51 −3.45 1998269 2.7 2.31 2.99 2.272.44 2.46 −2.46 2042056 2.5 5.46 −3.56 2046717 2.8 2048551 2.91 5.552055569 −2.76 −3.12 −3.33 −3.1 2055867 −3.4 −2.61 2.97 −2.67 21207433.25 2.97 2121863 2.76 2123516 8.29 4.6 3.89 3.71 2.66 3.83 2132285 2.942132774 2.7 2160794 −2.51 2195427 2.3 2.32 2201708 2.61 2208780 −2.412232658 2.25 2234853 −2.7 2241825 −2.39 2242817 3.4 2252107 2.44 22739442.48 2278688 −2.37 2293496 −2.88 2311213 −2.34 2343348 2.18 2.89 23526453.77 2360580 −4.5 −2.71 2365335 −2.67 2382192 −2.54 2382195 −2.872383269 −2.23 2394990 −2.83 2399162 −2.5 2446289 −2.15 2448149 −2.352453558 −2.4 2470485 −2.45 −2.8 2495131 2.22 2511277 3.07 2513883 4.473.82 3.93 3.67 17.42 2513883 3.35 2514988 4.03 2516448 2.88 2517254 2.652520894 3.21 2517386 2.51 2545486 −2.49 2550767 2.1 2579218 2.42 2607921−3.2 2538878 2.31 2636043 4.58 2660756 2.21 2.25 2675232 3.09 26953712.68 2708055 2.45 2740665 −2.54 2756333 2.66 2757583 2.8 4.75 4.03 4.134.93 4.31 33.5 2765271 2.25 2769888 −2.79 −3.17 −2.01 −3.37 2813255−2.72 2820337 2.29 2822027 3 2.96 2825358 2.44 2830828 −3.15 28314902.48 2860918 −3.2 2879068 2.67 2884613 2.54 2.46 2.51 2.2 2890336 −2.382891601 2.56 2899419 2.43 2912637 −2.38 −4.29 2912830 3.8 2921194 3.42921991 −3.1 −5.21 −4.67 −2.95 −3.43 2925373 −2.63 2929484 −2.89 29337754 5.14 4.73 4.32 6.47 2953987 3.13 2955163 2.33 3.24 2956444 2.1 3.042957205 2.94 2.44 2.35 2991027 2.9 2992044 3.07 2999855 2.4 3026540 2.653028719 −2.6 3038508 2.57 3070625 −2.67 3074113 3.03 3084204 −2.473108506 3.02 3109384 2.6 3120209 2.53 3121380 3.32 3121871 7.45 31237313.07 3128810 4.34 3129338 −2.86 3136857 −3.24 3158828 2.67 3170010 −3.673208425 2.54 3222802 2.71 2.55 2.4 3.23 3225977 2.89 2.59 3240708 2.023272165 −2.57 3284411 −2.4 3345528 4.11 3380034 −3.15 3381870 2.62 2.33407653 2.7 3427373 4.2 3472927 2.77 3493381 2.62 3493710 2.46 3494714−2.53 3606046 3.24 3679667 −2.09 3715059 −3.17 −4.3 3792988 3.23 3815422−3.78 4019706 2.99 3.55 4066764 −2.3 4070979 2.44 4087621 −3.55 40911862.45 2.64 4092112 3.55 4107126 2.88 4110976 2.18 4203937 7.13 42469668.12 3.03 4254855 2.3 4284384 2.73 4287327 −3.47 −3.14 2.66 −2.54 −2.144403805 2.4 4508879 2.86 2.68 4549259 2.53 4556538 2.53 3.02 2.454715924 −2.21 4721130 4.25 3.57 4795635 −2.38 5047895 −2.44 5077219−2.63 5093071 2.36 5102731 2.33 5266015 2.47 5266376 2.54 5293028 −2.35398014 −2.67 5398701 −3.55 5399371 2.63 −2.63 5512044 2.26 5541949 2.38

[0188] TABLE 2 NUCLEOIDE NUCLEOTIDE PROTEIN PROTEIN CLONE SEQ IDTEMPLATE SEQ ID TEMPLATE ID NO: ID NO: ID 26474 1 220060.4 60123 2016238.1 63038 3 1266683.1  72713 4   129384.1c 85606 5  3201389CB1 63201389CD1 86390 7   086390CB1 8 086390CD1 118501 9 1102322.16 118501 10 1545176CB1 11 1545176CD1 121785 12 978222.4 121785 13 978222.5 13607314  1720920CB1 15 1720920CD1 160822 16  1857017CB1 17 1857017CD1 349371016  1857017CB1 17 1857017CD1 167081 18  2114865CB1 19 2114865CD1 17202320  2700132CB1 21 2700132CD1 2470485 20  2700132CB1 21 2700132CD1 21138922 238349.2 211389 23   238349.4c 237027 24   402917.3c 259054 25406330.1 271299 26  2516070CB1 27 2516070CD1 2517386 26  2516070CB1 272516070CD1 279249 28   167507CB1 29 167507CD1 279898 30  3860413CB1 313860413CD1 3121871 30  3860413CB1 31 3860413CD1 280932 32  3393861CB1 333393861CD1 293477 34  2517374CB1 35 2517374CD1 311346 36 030850.7 31848637   237416.12c 318486 38  237416.14 341884 39  1269631CB1 40 1269631CD1348143 41   961189CB1 42 961189CD1 388964 43 246946.1 389362 44 017958.1407032 45 985556.1 408886 46   476301CB1 47 476301CD1 419492 48 996427.2437481 49  2989375CB1 50 2989375CD1 442723 51 236359.2 443991 52  011112.1c 450856 53 198268.1 452321 54 978740.3 454839 55 400197.1459372 56   235687.5c 460779 57  2797839CB1 58 2797839CD1 462069 59978690.6 480791 60 348072.5 481402 61   085596CB1 62 085596CD1 510056 63  103917CB1 64 103917CD1 511448 65  3603037CB1 66 3603037CD1 560115 67  088564CB1 68 088564CD1 604019 69 040429.1 630625 70 407096.2 669498 71 209265.54 701484 72   701484CB1 73 701484CD1 758192 74 251859.2 77315475  3766715CB1 76 3766715CD1 818192 77  2049950CB1 78 2049950CD1 81819279   231588.6c 872017 80 152298.2 891322 81 199507.1 963536 82 1434821CB1 83 1434821CD1 970905 84  289671.27 990375 85  1282225CB1 861282225CD1 1213932 87  263336.57 1259841 88  464689.40 1272483 89155943.1 1306814 90   243794.19c 1306814 91  243794.23 1308112 92  159309CB1 93 159309CD1 1315663 94  1273641CB1 95 1273641CD1 1316801 96403717.1 1326255 97 047593.1 1368834 98 347055.4 1379063 99  898899.111379063 100  898899.32 1381654 101  2047630CB1 102 2047630CD1 1395143103 1039889.8  1435374 104  1272969CB1 105 1272969CD1 1441245 106  282397.85c 1441245 107  282397.94 1448718 108  1448817CB1 1091448817CD1 1454436 110 1100769.2  1457424 111 332521.1 1457718 112 225080.16 1464613 113 334851.5 1468660 114 995529.7 1468660 115995529.8 1482116 116 201851.1 1495382 117   059509CB1 118 059509CD11500245 119  481231.14 1511658 120   280276CB1 121 280276CD1 1519431 122 4675668CB1 123 4675668CD1 1519683 124 153825.1 1522880 125   403484.2c1522880 126  1459432CB1 127 1459432CD1 1530595 128 1096583.1  1559665129   516300CB1 130 516300CD1 1559756 131   627856CB1 132 627856CD11560906 133  1823159CB1 134 1823159CD1 1577614 135 232567.4 1616783 136218419.1 1619292 137  1630551CB1 138 1630551CD1 1619980 139  360961.191623214 140   809809CB1 141 809809CD1 1630990 142  2558815CB1 1432558815CD1 1696224 144  242010.16 1696224 145  1678695CB1 146 1678695CD11705208 147 988653.1 1711151 148  1250434CB1 149 1250434CD1 1732221 150236196.3 1756875 151 442308.1 1786554 152 060957.1 1822716 153  014284CB1 154 014284CD1 1833362 155 1095192.1  1834236 156  233003.201834236 157  1911808CB1 158 1911808CD1 1838114 159 978276.8 1845046 160 405844.21 1845046 161  405844.22 1846209 162  2705515CB1 163 2705515CD11846463 164  2023119CB1 165 2023119CD1 1861456 166 1000084.27 3679667166 1000084.27 1867614 167 220134.1 1869130 168 216331.1 1871340 169206044.1 1874037 170  382906.16 1874307 171 331306.1 1890576 1721094829.20 1890576 173 1094829.38 1890791 174 1135580.4  1920215 175196623.3 1922468 176  048488.32 1926883 177  2767012CB1 178 2767012CD11930235 179  1651724CB1 180 1651724CD1 1956982 181 206397.1 1958226 182 461707.40 1963081 183  2706645CB1 184 2706645CD1 1966517 185 474372.71969563 186  3592543CB1 187 3592543CD1 1975268 188   048612.12c 1975268189  048612.13 1998269 190  245259.16 2042056 191   522433CB1 192522433CD1 2046717 193 1040667.43 2048551 194  2048551CB1 195 2048551CD12055569 196  1969731CB1 197 1969731CD1 2055867 198 1326983.14 2120743199  2120743CB1 200 2120743CD1 2121863 201  3551330CB1 202 3551330CD12123516 203  1440032CB1 204 1440032CD1 2132285 205 1000133.1  2132774206  4020439CB1 207 4020439CD1 2160794 208  2507087CB1 209 2507087CD12195427 210 239996.1 2201708 211 1097380.1  2208780 212   021524.2c2208780 213 021524.9 2232658 214  253987.16 2234853 215 344553.1 2241825216 410785.1 2242817 217 237623.6 2252107 218 076047.1 2273944 2191099500.15 2273944 220 1099500.18 2278688 221  2278688CB1 222 2278688CD12293496 223 380283.1 2311213 224  1720847CB1 225 1720847CD1 2343348 226  333776.1c 2352645 227  3478236CB1 228 3478236CD1 2360580 229 147541.17 2365335 230   331120.16c 2382192 231   575983CB1 232575983CD1 2382195 233 413268.6 2383269 234  1989186CB1 235 1989186CD12394990 236   337448.1c 2399162 237  228304.19 2446289 238  420527.252448149 239 998034.3 2453558 240  474165.26 2495131 241   697785CB1 242697785CD1 2511277 243 346209.3 2513883 244   167772CB1 245 167772CD12514988 246  2514988CB1 247 2514988CD1 2516070 248  481231.16 2516070249  481231.17 2516104 249  481231.17 2516261 249  481231.17 2516448 249 481231.17 2517254 250 1045853.2  5398014 250 1045853.2  2520894 251336615.1 2527879 252 1328423.2  2545486 253 085282.1 2550767 2541081605.3  2579218 255 1053517.1  2607921 256  480169.76 2636043 257 2636043CB1 258 2636043CD1 2641522 259  2993696CB1 260 2993696CD12660756 261  240518.21 2660756 262  240518.34 2663164 263   001322.4c2675232 264 350502.3 2675232 265   350502.4c 2695371 266 253783.32708055 267 085119.1 2740665 268 902559.1 2756333 269  4113161CB1 2704113161CD1 2757583 271  2757583CB1 272 2757583CD1 2765271 273 198317.12769888 274  1508254CB1 275 1508254CD1 2813255 276 474691.3 2820337 277 2457215CB1 278 2457215CD1 2822027 279   201395.4c 2825358 280 233189.21 2830828 281   196606.6c 2830828 282   196606.8c 2831490 2831040190.3  2860918 284  1427459CB1 285 1427459CD1 2879068 286  480453.16c 2884613 287 1095604.1  2890336 288  241291.28 2891601 289230611.1 2899419 290  3993708CB1 291 3993708CD1 2899419 292 1000133.122912637 293   400253.17c 2912637 294 400253.5 2912830 295   030882CB1296 030882CD1 2921194 297   898779CB1 298 898779CD1 2921991 299 3727408CB1 300 3727408CD1 2925373 301   984236.1c 2925373 302  984236.2c 2929484 303 348082.5 2929484 304 348082.7 2933775 3051097910.1  2953987 306 246841.1 2955163 307 351241.1 2956444 308 2790762CB1 309 2790762CD1 2957205 310  2253717CB1 311 2253717CD12991027 312  2655184CB1 313 2655184CD1 2991027 314   363000.9c 2992044315  232818.15 2999855 316  347781.10 2999855 317  2477616CB1 3182477616CD1 3026540 319 360532.1 3026540 320 360532.9 3028719 321110245.1 3038508 322  478620.53 3038508 323  1813444CB1 324 1813444CD13070625 325  474588.21 3074113 326 407838.1 3084204 327  994387.193108506 328 347796.7 3109384 329   406498.4c 3120209 330  3346307CB1 3313346307CD1 3121380 332  4005778CB1 333 4005778CD1 3123731 334  995575.173128810 335   863406CB1 336 863406CD1 3129338 337  413864.17 3136857 338 350106.16 3158828 339 399785.1 3170010 340  010498.19 3208425 341 255824.39 3208425 342  2706606CB1 343 2706606CD1 3222802 344 118006.13225977 345 1039889.26 3240708 346 481480.7 3272165 347   662575CB1 348662575CD1 3284411 349 027619.3 3345528 350 235447.5 3380034 351 331104.23381870 352 348390.2 3407653 353 127004.1 3427373 354 026190.1 3472927355 250330.1 3493381 356  480375.28 3494714 357  364726.10 3494714 358 364726.12 3606046 359  1505038CB1 360 1505038CD1 3715059 361  903508.123792988 362   346716.17c 3792988 363   346716.21c 3815422 364 330776.14019706 365   407999.1c 4066764 366  1719478CB1 367 1719478CD1 4070979368 351157.2 4087621 369   088957CB1 370 088957CD1 5398701 369  088957CB1 370 088957CD1 4091186 371 980446.1 4092112 372 198827.14107126 373 1102297.22 4110976 374 215112.1 4203937 375 171495.1 4246966376  242010.43 4254855 377  5834958CB1 378 5834958CD1 4284384 379  335648.1c 4287327 380 333840.1 4403805 381 480885.2 4508879 382  998106.8c 4549259 383 400701.4 4556538 384 1100320.4  4715924 385 246727.11 4715924 386  246727.17 4721130 387   1102322.12c 4721130 3881102322.18 4795635 389  2070610CB1 390 2070610CD1 5047895 391 336733.35077219 392 1326902.13 5077219 393 1326902.6  5093071 394  013521.165102731 395 985369.1 5266015 396 002455.1 5266376 397 372647.1 5293028398 208075.1 5399371 399 209279.1 5512044 400 381058.1 5541949 401046977.1

[0189] TABLE 3 SEQ ID TEMPLATE GI NO: ID Number E-value Annotation 1220060.4 g847737 0 Human transthyretin precursor mRNA, complete cds. 2016238.1 g187326 0 Human macrophage mannose receptor (MRC1) gene, exon24. 3 1266683.1  g1103903 0 Human spermidine/spermineN1-acetyltransferase (SSAT) gene, complete cds. 4   129384.1c g508989 0Human (oct-6) mRNA, complete cds. 5  3201389CB1 g927210 0 Human mRNA foradrenergic receptor alpha 1C isoform 3, complete cds. 6  3201389CD1 g927210 0 Human mRNA for adrenergic receptor alpha 1C isoform 3,complete cds. 7   086390CB1 g337749 0 Human serum amyloid A proteinmRNA, complete cds. 8    086390CD1 g337749 0 Human serum amyloid Aprotein mRNA, complete cds. 9 1102322.16 g313283 0 African green monkeyhsp70 mRNA. 10  1545176CB1 g313283 0 African green monkey hsp70 mRNA. 11 1545176CD1  g313283 0 African green monkey hsp70 mRNA. 12 978222.4g6006501 0 Human mRNA for basic-helix-loop-helix protein, bHLH (Hey2gene). 13 978222.5 g600650l 0 Human mRNA for basic-helix-loop-helixprotein, bHLH (Hey2 gene). 14  1720920CB1 g1617313 0 Human mRNA formelanoma-associated chondroitin sulfate proteoglycan (MCSP). 15 1720920CD1  g1617313 0 Human mRNA for melanoma-associated chondroitinsulfate proteoglycan (MCSP). 16  1857017CB1 g184243 0 Human3-hydroxy-3-methylglutaryl CoA reductase mRNA, complete cds. 17 1857017CD1  g184243 0 Human 3-hydroxy-3-methylglutaryl CoA reductasemRNA, complete cds. 18  2114865CB1 g177808 0 Humanalpha-1-antichymotrypsin (AACT) mRNA, complete cds. 19  2114865CD1 g177808 0 Human alpha-1-antichymotrypsin (AACT) mRNA, complete cds. 20 2700132CB1 g415818 0 Human mki67a mRNA (long type) for antigen ofmonoclonal antibody Ki-67. 21  2700132CD1  g415818 0 Human mki67a mRNA(long type) for antigen of monoclonal antibody Ki-67. 22 238349.2g4324682 E−104 late gestation lung protein 1 [Rattus norvegicus] 23  238349.4c g7644416 0.4 Mus platythrix TSPY gene, intron 1. 24  402917.3c Incyte Unique 25 406330.1 g182103 0 Human enkephalin B(enkB) gene, exon 4 and 3′ flank and complete cds. 26  2516070CB1 g287710 Human mRNA for apolipoprotein AI (apo AI)=. 27  2516070CD1  g28771 0Human mRNA for apolipoprotein AI (apo AI)=. 28   167507CB1 g177889 0Human alpha-2-thiol protease inhibitor mRNA, complete coding sequence.29    167507CD1 g177889 0 Human alpha-2-thiol protease inhibitor mRNA,complete coding sequence. 30  3860413CB1 g187530 0 Humanmetallothionein-II pseudogene (mt-IIps). 31  3860413CD1  g187530 0 Humanmetallothionein-II pseudogene (mt-IIps). 32  3393861CB1 g182429 0 Humanfibrinogen beta-chain mRNA, partial cds. 33  3393861CD1  g182429 0 Humanfibrinogen beta-chain mRNA, partial cds. 34  2517374CB1 g24444 0 HumanmRNA for alpha1-acid glycoprotein (orosomucoid). 35  2517374CD1  g244440 Human mRNA for alpha1-acid glycoprotein (orosomucoid). 36 030850.7Incyte Unique 37   237416.12c g396704 5.00E−92 Human integrin associatedprotein mRNA, complete cds,. 38  237416.14 g396704 0 Human integrinassociated protein mRNA, complete cds,. 39  1269631CB1 g5030423 0 Humangp250 precursor, mRNA, complete cds. 40  1269631CD1  g5030423 0 Humangp250 precursor, mRNA, complete cds. 41   961189CB1 g286008 0 Human mRNAfor KIAA0020 gene, complete cds. 42    961189CD1 g286008 0 Human mRNAfor KIAA0020 gene, complete cds. 43 246946.1 g4107230 3.00E−34 HumanmRNA for lipophilin B. 44 017958.1 Incyte Unique 45 985556.1 IncyteUnique 46   476301CB1 g1232174 0 Human mRNA for transketolase-likeprotein (2418 bp). 47    476301CD1 g1232174 0 Human mRNA fortransketolase-like protein (2418 bp). 48 996427.2 g179892 0 Human cAMPphosphodiesterase PDE7 (PDE7A1) mRNA, complete cds. 49  2989375CB1Incyte Unique 50  2989375CD1  Incyte Unique 51 236359.2 Incyte Unique 52  011112.1c g3183903 0 Human partial mRNA; ID YG40-1B. 53 198268.1g4337095 0 Human MSH55 gene, partial cds; and CLIC1, DDAH, G6b, G6c,G5b, G6d, G6e, G6f, BAT5, G5b, CSK: 54 978740.3 Incyte Unique 55400197.1 g1457944 5.00E−10 Human desmoglein 3 gene, promoter region. 56  235687.5c Incyte Unique 57  2797839CB1 g189421 0 Humanproliferating-cell nucleolar protein P120 mRNA, complete cds. 58 2797839CD1  g189421 0 Human proliferating-cell nucleolar protein P120mRNA, complete cds. 59 978690.6 g3287264 e−145 Rattus norvegicus mRNAfor STOP protein. 60 348072.5 g288562 0 Human mRNA forinter-alpha-trypsin inhibitor heavy chain H3. 61   085596CB1 g184391 0Human histidine-rich glycoprotein mRNA, complete cds. 62    085596CD1g184391 0 Human histidine-rich glycoprotein mRNA, complete cds. 63  103917CB1 g183030 0 Human grancalcin mRNA, complete cds. 64   103917CD1 g183030 0 Human grancalcin mRNA, complete cds. 65 3603037CB1 g181986 0 Human early growth response 2 protein (EGR2) mRNA,complete cds. 66  3603037CD1  g181986 0 Human early growth response 2protein (EGR2) mRNA, complete cds. 67   088564CB1 g1778716 0 Humanchemokine exodus-1 mRNA, complete cds. 68    088564CD1 g1778716 0 Humanchemokine exodus-1 mRNA, complete cds. 69 040429.1 Incyte Unique 70407096.2 g1237037 0 Human mRNA for thioredoxin reductase. 71  209265.54g2160718 0 Human amphiphysin II mRNA, complete cds. 72   701484CB1g5926690 0 Human genomic DNA, chromosome 6p21.3, HLA Class I region,section 2/20. 73    701484CD1 g5926690 0 Human genomic DNA, chromosome6p21.3, HLA Class I region, section 2/20. 74 251859.2 g1145815 0 Human54 kDa progesterone receptor-associated immunophilin FKBP54 mRNA,partial cds. 75  3766715CB1 g4914599 0 Human mRNA; cDNA DKFZp564A126(from clone DKFZp564A126); partial cds. 76  3766715CD1  g4914599 0 HumanmRNA; cDNA DKFZp564A126 (from clone DKFZp564A126); partial cds. 77 2049950CB1 g183038 0 Human gamma-glutamylcysteine synthetase (GCS)mRNA, complete cds. 78  2049950CD1  g183038 0 Humangamma-glutamylcysteine synthetase (GCS) mRNA, complete cds. 79  231588.6c g183038 0 Human gamma-glutamylcysteine synthetase (GCS)mRNA, complete cds. 80 152298.2 Incyte Unique 81 199507.1 Incyte Unique82  1434821CB1 g35706 0 Human pS2 mRNA induced by estrogen from Humanbreast cancer cell line MCF-7. 83  1434821CD1  g35706 0 Human pS2 mRNAinduced by estrogen from Human breast cancer cell line MCF-7. 84 289671.27 g31896 0 Human GPx-3 mRNA for plasma glutathione peroxidase.85  1282225CB1 g182355 0 Human liver fatty acid binding protein (FABP)mRNA, complete cds. 86  1282225CD1  g182355 0 Human liver fatty acidbinding protein (FABP) mRNA, complete cds. 87  263336.57 g187538 0 Humanmetallothionein-Ie gene (hMT-Ie). 88  464689.40 g30257 0 Human CST3 genefor cystatin C. 89 155943.1 g6453599 0 Human mRNA; cDNA DKFZp434K098(from clone DKFZp434K098); partial cds. 90   243794.19c g550026 0 Humanribosomal protein S29 mRNA, complete cds. 91  243794.23 g550026 0 Humanribosomal protein S29 mRNA, complete cds. 92   159309CB1 g510689 0 HumanKi nuclear autoantigen mRNA, complete cds. 93    159309CD1 g510689 0Human Ki nuclear autoantigen mRNA, complete cds. 94  1273641CB1 IncyteUnique 95  1273641CD1  Incyte Unique 96 403717.1 Incyte Unique 97047593.1 Incyte Unique 98 347055.4 g410027 0 Human3-hydroxy-3-methylglutaryl CoA synthase mRNA, complete cds. 99 898899.11 g183976 0 Human hepatocyte growth factor-like protein mRNA,complete cds. 100  898899.32 g1311660 0 Human hepatocyte growthfactor-like protein gene, complete cds. 101  2047630CB1 g179099 0 Humanasparagine synthetase mRNA, complete cds. 102  2047630CD1  g179099 0Human asparagine synthetase mRNA, complete cds. 103 1039889.8  g178042 0Human cytoskeletal gamma-actin gene, complete cds. 104  1272969CB1g286028 0 Human mRNA for XPAC protein. 105  1272969CD1  g286028 0 HumanmRNA for XPAC protein. 106   282397.85c g3660662 0 Human D15F37pseudogene, S3 allele, mRNA sequence. 107  282397.94 g6683696 0 HumanmRNA for KIAA0393 protein, partial cds. 108  1448817CB1 g183117 0 Humaninsulin-like growth factor binding protein mRNA, complete cds. 109 1448817CD1  g183117 0 Human insulin-like growth factor binding proteinmRNA, complete cds. 110 1100769.2  g296451 0 Human mRNA for ribosomalprotein S26. 111 332521.1 Incyte Unique 112  225080.16 g951313 0 Human2,3-oxidosqualene-lanosterol cyclase mRNA, complete cds. 113 334851.5g5912050 0 Human mRNA; cDNA DKFZp434P1550 (from clone DKFZp434P1550);partial cds. 114 995529.7 g3126638 0 Human mRNA for CDC2 delta T,complete cds. 115 995529.8 g29838 0 Human CDC2 gene involved in cellcycle control. 116 201851.1 g2104768 0 Human echinodermmicrotubule-associated protein homolog HuEMAP mRNA, complete cds. 117  059509CB1 g1149557 0 Human TNF-related apoptosis inducing ligand TRAILmRNA, complete cds. 118    059509CD1 g1149557 0 Human TNF-relatedapoptosis inducing ligand TRAIL mRNA, complete cds. 119  481231.14g28771 0 Human mRNA for apolipoprotein AI (apo AI)=. 120   280276CB1g182406 0 Human fibrinogen alpha subunit and fibrinogen alpha subunitprecursor, genes, complete cds. 121    280276CD1 g182406 0 Humanfibrinogen alpha subunit and fibrinogen alpha subunit precursor, genes,complete cds. 122  4675668CB1 g1160618 0 Human bystin mRNA, completecds. 123  4675668CD1  g1160618 0 Human bystin mRNA, complete cds. 124153825.1 g456256 0 Human stromelysin-3 mRNA. 125   403484.2c g1737178 0Human somatostatin receptor-like protein (GPR24) gene, complete cds. 126 1459432CB1 g1737178 0 Human somatostatin receptor-like protein (GPR24)gene, complete cds. 127  1459432CD1  g1737178 0 Human somatostatinreceptor-like protein (GPR24) gene, complete cds. 128 1096583.1  g303409.00E−96 Human gene for cytochrome P(1)-450. 129   516300CB1 g1098616 0Human CD94 protein mRNA, complete cds. 130    516300CD1 g1098616 0 HumanCD94 protein mRNA, complete cds. 131   627856CB1 g2665518 0 Humantyrosyl-tRNA synthetase mRNA, complete cds. 132    627856CD1 g2665518 0Human tyrosyl-tRNA synthetase mRNA, complete cds. 133  1823159CB1g1378039 0 Human myotubularin (MTM1) mRNA, complete cds. 134 1823159CD1  g1378039 0 Human myotubularin (MTM1) mRNA, complete cds.135 232567.4 g182718 0 Human follistatin gene, exons 1-5. 136 218419.1Incyte Unique 137  1630551CB1 g30302 0 Human mRNA for cytochrome c1. 138 1630551CD1  g30302 0 Human mRNA for cytochrome c1. 139  360961.19g896282 0 Human methionine adenosyltransferase alpha subunit genefragment. 140   809809CB1 g3252871 0 Human BRCA1-associated protein 2(BRAP2) mRNA, complete cds. 141    809809CD1 g3252871 0 HumanBRCA1-associated protein 2 (BRAP2) mRNA, complete cds. 142  2558815CB1g1049218 0 Human gamma-aminobutyraldehyde dehydrogenase mRNA, completecds. 143  2558815CD1  g1049218 0 Human gamma-aminobutyraldehydedehydrogenase mRNA, complete cds. 144  242010.16 g188487 0 Human MHCclass III HSP70-1 gene (HLA), complete cds. 145  1678695CB1 g5926690 0Human genomic DNA, chromosome 6p21.3, HLA Class I region, section 2/20.146  1678695CD1  g5926690 0 Human genomic DNA, chromosome 6p21.3, HLAClass I region, section 2/20. 147 988653.1 g31129 0 Human mRNA for earlygrowth response protein 1 (hEGR1). 148  1250434CB1 g1144012 0 Human MOP1mRNA, complete cds. 149  1250434CD1  g1144012 0 Human MOP1 mRNA,complete cds. 150 236196.3 g4003383 0 Human genomic DNA of 8p21.3-p22anti-oncogene of hepatocellular colorectal and non-small cell lung c 151442308.1 g3955193 0 Human homeodomain protein (Nkx2.2) gene, exon 2 andcomplete cds. 152 060957.1 Incyte Unique 153   014284CB1 g1006656 0Human mRNA for cathepsin C. 154    014284CD1 g1006656 0 Human mRNA forcathepsin C. 155 1095192.1  g57216 2.00E−75 Rat brain mRNA for sodiumchannel protein I. 156  233003.20 Incyte Unique 157  1911808CB1 IncyteUnique 158  1911808CD1  Incyte Unique 159 978276.8 Incyte Unique 160 405844.21 g179320 0 Human B61 mRNA, complete cds. 161  405844.22g179320 0 Human B61 mRNA, complete cds. 162  2705515CB1 g30820 0 HumanmRNA for IFN-inducible gamma2 protein. 163  2705515CD1  g30820 0 HumanmRNA for IFN-inducible gamma2 protein. 164  2023119CB1 g306769 0 Humanleukemia virus receptor 1 (GLVR1) mRNA, complete cds. 165  2023119CD1 g306769 0 Human leukemia virus receptor 1 (GLVR1) mRNA, complete cds.166 1000084.27 g3719220 0 Human vascular endothelial growth factor mRNA,complete cds. 167 220134.1 g1546096 0 Human hbc647 mRNA sequence. 168216331.1 Incyte Unique 169 206044.1 g4529920 3.50E−17 serine proteaseinhibitor 170  382906.16 g180142 0 Human CD53 glycoprotein mRNA,complete cds. 171 331306.1 g219862 0 Human mRNA for HM145. 1721094829.20 g181040 0 Human cAMP response element regulatory protein(CREB2) mRNA, complete cds. 173 1094829.38 g220087 0 Human mRNA for DNAbinding protein TAXREB67. 174 1135580.4  g2887408 0 Human KIAA0417 mRNA,complete cds. 175 196623.3 g4929830 0 Human peroxisomal D3,D2-enoyl-CoAisomerase (PEC1) mRNA, complete cds. 176  048488.32 g1503985 0 HumanmRNA for KIAA0201 gene, complete cds. 177  2767012CB1 g306713 0 Humanheat shock protein, E. coli DnaJ homologue mRNA, complete cds. 178 2767012CD1  g306713 0 Human heat shock protein, E. coli DnaJ homologuemRNA, complete cds. 179  1651724CB1 g35135 0 Human odc1 mRNA forornithine decarboxylase. 180  1651724CD1  g35135 0 Human odc1 mRNA forornithine decarboxylase. 181 206397.1 g3719360 2.00E−34 Human CCchemokine gene cluster, complete sequence. 182  461707.40 g6841321 0Human HSPC336 mRNA, partial cds. 183  2706645CB1 g337728 0 Human S100protein beta-subunit gene, exon 3. 184  2706645CD1  g337728 0 Human S100protein beta-subunit gene, exon 3. 185 474372.7 g1066790 0 Human proteinkinase-related oncogene (PIMI) mRNA, complete cds. 186  3592543CB1g186624 0 Human c-jun proto oncogene (JUN), complete cds, clone hCJ-1.187  3592543CD1  g186624 0 Human c-jun proto oncogene (JUN), completecds, clone hCJ-1. 188   048612.12c g307332 0 Human phosphoenolpyruvatecarboxykinase (PCK1) gene, complete cds with repeats. 189  048612.13g189944 0 Human (clone lamda-hPEC-3) phosphoenolpyruvate carboxykinase(PCK1) mRNA, complete cds. 190  245259.16 g36031 0 Human rhoB gene mRNA.191   522433CB1 g1813326 0 Human mRNA for TGF-beta superfamily protein,complete cds. 192    522433CD1 g1813326 0 Human mRNA for TGF-betasuperfamily protein, complete cds. 193 1040667.43 g28338 5.00E−94 HumanmRNA for cytoskeletal gamma-actin. 194  2048551CB1 g188709 0 Humanmetallothionein I-B gene, exon 3. 195  2048551CD1  g188709 0 Humanmetallothionein I-B gene, exon 3. 196  1969731CB1 g2344811 0 Human mRNAfor Drg1 protein. 197  1969731CD1  g2344811 0 Human mRNA for Drg1protein. 198 1326983.14 Incyte Unique 199  2120743CB1 Incyte Unique 200 2120743CD1  Incyte Unique 201  3551330CB1 g719268 0 Human cysteine-richheart protein (hCRHP) mRNA, complete cds. 202  3551330CD1  g719268 0Human cysteine-rich heart protein (hCRHP) mRNA, complete cds. 203 1440032CB1 g35221 0 Human heat-shock protein HSP70B′ gene. 204 1440032CD1  g35221 0 Human heat-shock protein HSP70B′ gene. 2051000133.1  g339660 0 Human thymosin beta 10 mRNA, complete cds. 206 4020439CB1 g296451 0 Human mRNA for ribosomal protein S26. 207 4020439CD1  g296451 0 Human mRNA for ribosomal protein S26. 208 2507087CB1 g6807670 0 Human mRNA; cDNA DKFZp434F205 (from cloneDKFZp434F205); complete cds. 209  2507087CD1  g6807670 0 Human mRNA;cDNA DKFZp434F205 (from clone DKFZp434F205); complete cds. 210 239996.1Incyte Unique 211 1097380.1  g6594626 0 Human pRGR1 mRNA, partial cds.212   021524.2C g598639 7.00E−77 Human HepG2 3′ region Mbol cDNA, clonehmd2d06m3. 213 021524.9 g598640 2.00E−09 Human HepG2 partial cDNA, clonehmd2d06m5. 214  253987.16 g313212 0 Human Id3 gene for HLH typetranscription factor. 215 344553.1 g469095 0 Human RNA for MTP. 216410785.1 g187133 0 Human liver glucose transporter-like protein (GLUT2),complete cds. 217 237623.6 g402482 0 Human secretory protein (P1.B)mRNA, complete cds. 218 076047.1 g1688257 0 Human collagenase andstromelysin genes, complete cds, and metalloelastasegene, partial cds.219 1099500.15 g3287488 0 Human Hsp89-alpha-delta-N mRNA, complete cds.220 1099500.18 g32487 0 Human mRNA for 90-kDa heat-shock protein. 221 2278688CB1 g4210725 0 Human mRNA for puromycin sensitiveaminopeptidase, partial. 222  2278688CD1  g4210725 0 Human mRNA forpuromycin sensitive aminopeptidase, partial. 223 380283.1 g2564321 0Human mRNA for KIAA0287 gene, partial cds. 224  1720847CB1 g42184256.00E−11 Human pex3 gene (joined cds, promoter and exon 1). 225 1720847CD1  g4218425 6.00E−11 Human pex3 gene (joined cds, promoter andexon 1). 226   333776.1c Incyte Unique 227  3478236CB1 g179039 0 Humanamphiregulin (AR) mRNA, complete cds, clones lambda-AR1 and lambda-AR2.228  3478236CD1  g179039 0 Human amphiregulin (AR) mRNA, complete cds,clones lambda-AR1 and lambda-AR2. 229  147541.17 g6899845 0 Human mRNAfor cisplatin resistance-associated overexpressed protein, complete cds.230   331120.16c g663009 0 Human PHKLA mRNA. 231   575983CB1 g2546963 0Human mRNA for diubiquitin. 232    575983CD1 g2546963 0 Human mRNA fordiubiquitin. 233 413268.6 g541677 0 Human HBZ17 mRNA. 234  1989186CB1g2708328 0 Human atrophin-1 interacting protein 4 (AIP4) mRNA, partialcds. 235  1989186CD1  g2708328 0 Human atrophin-1 interacting protein 4(AIP4) mRNA, partial cds. 236   337448.1c g5912019 0 Human mRNA; cDNADKFZp434H0735 (from clone DKFZp434H0735); partial cds. 237  228304.19Incyte Unique 238  420527.25 g186757 0 Human protein kinase mRNA. 239998034.3 g927597 0 Human transcription factor TFIIIB 90 kDa subunit(hTFIIIB90) mRNA, complete cds. 240  474165.26 g3005586 0 HumanSer/Arg-related nuclear matrix protein (SRM160) mRNA, complete cds. 241  697785CB1 g187109 0 Human 14 kd lectin mRNA, complete cds. 242   697785CD1 g187109 0 Human 14 kd lectin mRNA, complete cds. 243346209.3 g4240220 3.00E−14 Human mRNA for KIAA0866 protein, completecds. 244   167772CB1 g3954884 0 Human mRNA for Ig kappa light chain,anti-RhD, therad 7. 245    167772CD1 g3954884 0 Human mRNA for Ig kappalight chain, anti-RhD, therad 7. 246  2514988CB1 g178848 0 Humanapolipoprotein E mRNA, complete cds. 247  2514988CD1  g178848 0 Humanapolipoprotein E mRNA, complete cds. 248  481231.16 g28771 0 Human mRNAfor apolipoprotein AI (apo AI)=. 249  481231.17 g28771 0 Human mRNA forapolipoprotein AI (apo AI)=. 250 1045853.2  g763428 0 Human mRNA clonewith similarity to L-glycerol-3-phosphate:NAD oxidoreductase and albumingene se 251 336615.1 g2072161 0 Human tubby related protein 1 (TULP1)mRNA, complete cds. 252 1328423.2  g682747 0 Human mRNA for Apol_Human(MER5(Aopl-Mouse)-like protein), complete cds. 253 085282.1 IncyteUnique 254 1081605.3  g6466185 0 Human zinc finger protein ZNF228(ZNF228) mRNA, complete cds. 255 1053517.1  g7339817 0.15 Mus musculusDNA methyltransferase (Dnmt1) gene, exon 28. 256  480169.76 g2921872 0Human spleen mitotic checkpoint BUB3 (BUB3) mRNA, complete cds. 257 2636043CB1 Incyte Unique 258  2636043CD1  Incyte Unique 259  2993696CB1g1143491 0 Human mRNA for BiP protein. 260  2993696CD1  g1143491 0 HumanmRNA for BiP protein. 261  240518.21 g6841489 1.00E−80 Human HSPC134mRNA, complete cds. 262  240518.34 g6841489 0 Human HSPC134 mRNA,complete cds. 263   001322.4c Incyte Unique 264 350502.3 g39781704.00E−36 Mus musculus lysyl oxidase-related protein 2 (Lor2) mRNA, 265  350502.4c g2661055 6.00E−25 Human clone 23863 mRNA, partial cds. 266253783.3 g2664429 6.40E−43 hypothetical protein 267 085119.1 g1000863 0Human DNA-binding protein (Fli-1) gene, 5′ end of cds. 268 902559.1g183990 0 Human epidermal growth factor receptor (HER3) mRNA, completecds. 269  4113161CB1 g3360429 0 Human clone 23929 mRNA sequence. 270 4113161CD1  g3360429 0 Human clone 23929 mRNA sequence. 271  2757583CB1g187542 0 Human metallothionein (MT)I-F gene, complete cds. 272 2757583CD1  g187542 0 Human metallothionein (MT)I-F gene, complete cds.273 198317.1 g183398 3.00E−36 Human guanine nucleotide-binding proteinalpha-subunit gene (G-s-alpha), exon 2. 274  1508254CB1 g587201 0 HumanHK2 mRNA for hexokinase II. 275  1508254CD1  g587201 0 Human HK2 mRNAfor hexokinase II. 276 474691.3 Incyte Unique 277  2457215CB1 g38457 0Human mRNA for PTB-associated splicing factor. 278  2457215CD1  g38457 0Human mRNA for PTB-associated splicing factor. 279   201395.4c g22246260 Human mRNA for KIAA0343 gene, complete cds. 280  233189.21 g189869 0Human phosphoglycerate mutase 2 (muscle specific isozyme) (PGAM2) gene,5′ end. 281   196606.6C g2924334 0 Human mRNA for exportin (tRNA). 282  196606.8c g2924334 0 Human mRNA for exportin (tRNA). 283 1040190.3 g187518 0 Human MEM-102 glycoprotein mRNA, complete cds. 284  1427459CB1g2437832 0 Human mRNA for RNF3A (DONG1) ring finger protein. 285 1427459CD1  g2437832 0 Human mRNA for RNF3A (DONG1) ring fingerprotein. 286   480453.16c g4512253 0 Human gene for JKTBP2, JKTBP1,complete cds. 287 1095604.1  g1143491 0 Human mRNA for BiP protein. 288 241291.28 g3327107 0 Human mRNA for KIAA0647 protein, partial cds. 289230611.1 g1321847 4.00E−28 Human mRNA for U61 small nuclear RNA. 290 3993708CB1 g339660 0 Human thymosin beta 10 mRNA, complete cds. 291 3993708CD1  g339660 0 Human thymosin beta 10 mRNA, complete cds. 2921000133.12 g264772 0 thymosin beta-10 [Human, metastatic melanoma cellline, mRNA, 453 nt]. 293   400253.17c g6016843 5.00E−23 Human genomicDNA, chromosome 22q11.2, clone KB1561E1. 294 400253.5 g2826476 1.00E−13IL-17 receptor [Homo sapiens] 295   030882CB1 g1617087 0 Human mRNA forhBD-1 protein. 296    030882CD1 g1617087 0 Human mRNA for hBD-1 protein.297   898779CB1 g179530 0 Human IgE-binding protein (epsilon-BP) mRNA,complete cds. 298    898779CD1 g179530 0 Human IgE-binding protein(epsilon-BP) mRNA, complete cds. 299  3727408CB1 g189944 0 Human (clonelamda-hPEC-3) phosphoenolpyruvate carboxykinase (PCK1) mRNA, completecds. 300  3727408CD1  g189944 0 Human (clone lamda-hPEC-3)phosphoenolpyruvate carboxykinase (PCK1) mRNA, complete cds. 301  984236.1c Incyte Unique 302   984236.2c Incyte Unique 303 348082.5g3868777 Rattus norvegicus mRNA for atypical PKC specific binding 304348082.7 g3868778 0 atypical PKC specific binding protein [Rattusnorvegicus] 305 1097910.1  g181275 0 Human cytochrome P1-450(TCDD-inducible) mRNA, complete cds. 306 246841.1 g6453594 0 Human mRNA;cDNA DKFZp566M0947 (from clone DKFZp566M0947). 307 351241.1 g29354834.00E−56 Human minisatellite ceb 1 repeat region. 308  2790762CB1 IncyteUnique 309  2790762CD1  Incyte Unique 310  2253717CB1 g7542489 Homosapiens FK506 binding protein precursor (FKBP22) 311  2253717CD1  IncyteUnique 312  2655184CB1 g5531903 0 Human pre-mRNA splicing factor (SFRS3)mRNA, complete cds. 313  2655184CD1  g5531903 0 Human pre-mRNA splicingfactor (SFRS3) mRNA, complete cds. 314   363000.9c g5531903 0 Humanpre-mRNA splicing factor (SFRS3) mRNA, complete cds. 315  232818.15g3329377 0 Human vacuolar H(+)-ATPase subunit mRNA, complete cds. 316 347781.10 g1051169 0 Human GAP SH3 binding protein mRNA, complete cds.317  2477616CB1 g1051169 0 Human GAP SH3 binding protein mRNA, completecds. 318  2477616CD1  g1051169 0 Human GAP SH3 binding protein mRNA,complete cds. 319 360532.1 g37207 0 Human mRNA for slow skeletaltroponin C (TnC). 320 360532.9 g37207 0 Human mRNA for slow skeletaltroponin C (TnC). 321 110245.1 g3213194 0 Human serine-threonine kinase(BTAK) gene, partial cds. 322  478620.53 g386156 0 TLS = translocated inliposarcoma [Human, mRNA, 1824 nt]. 323  1813444CB1 g386158 0 TLS/CHOP =hybrid gene {translocation breakpoint} [Human, myxoid liposarcomascells, mRNA Mutant, 324  1813444CD1  g386158 0 TLS/CHOP = hybrid gene{translocation breakpoint} [Human, myxoid liposarcomas cells, mRNAMutant, 325  474588.21 g339700 0 Human polyadenylate binding protein(TIA-1) mRNA, complete cds. 326 407838.1 Incyte Unique 327  994387.19g6808610 2.00E−14 Human 88-kDa Golgi protein (GM88) mRNA, complete cds.328 347796.7 g710405 2.8 35 kDa protein [Bartonella henselae] 329  406498.4c Incyte Unique 330  3346307CB1 Incyte Unique 331  3346307CD1 Incyte Unique 332  4005778CB1 g182513 0 Human ferritin L chain mRNA,complete cds. 333  4005778CD1  g182513 0 Human ferritin L chain mRNA,complete cds. 334  995575.17 g189066 0 Human NAP (nucleosome assemblyprotein) mRNA, complete cds. 335   863406CB1 g3327203 0 Human mRNA forKIAA0695 protein, complete cds. 336    863406CD1 g3327203 0 Human mRNAfor KIAA0695 protein, complete cds. 337  413864.17 Incyte Unique 338 350106.16 g183059 0 Human glutamate dehydrogenase (GDH) mRNA, completecds. 339 399785.1 Incyte Unique 340  010498.19 g4240316 0 Human mRNA forKIAA0914 protein, complete cds. 341  255824.39 g28596 0 Human fibroblastmRNA for aldolase A. 342  2706606CB1 g178350 0 Human aldolase A mRNA,complete cds. 343  2706606CD1  g178350 0 Human aldolase A mRNA, completecds. 344 118006.1 g2290764 5.00E−86 Human gonadotropin releasing hormonereceptor (GNRHR) gene, exon 1. 345 1039889.26 g28338 0 Human mRNA forcytoskeletal gamma-actin. 346 481480.7 g561665 0 Human cysteine proteaseCPP32 isoform alpha mRNA, complete cds. 347   662575CB1 Incyte Unique348    662575CD1 Incyte Unique 349 027619.3 Incyte Unique 350 235447.5g37432 0 Human mRNA for transferrin receptor. 351 331104.2 g451209 0Human mRNA for histidase, complete cds. 352 348390.2 g36502 0 Human mRNAfor enteric smooth muscle gamma-actin. 353 127004.1 Incyte Unique 354026190.1 Incyte Unique 355 250330.1 g456587 4.00E−80 Humangranulocyte-macrophage colony stimulating factor (GM-CSF) receptor alphasubunit gene, exon 1 356  480375.28 g5360203 5.00E−27 Human A-kinaseanchor protein (AKAP100) mRNA, complete cds. 357  364726.10 g498012 0Human X104 mRNA, complete cds. 358  364726.12 g498012 0 Human X104 mRNA,complete cds. 359  1505038CB1 g536897 0 Human follistatin-relatedprotein precursor mRNA, complete cds. 360  1505038CD1  g536897 0 Humanfollistatin-related protein precursor mRNA, complete cds. 361  903508.12g5262490 0 Human mRNA; cDNA DKFZp564D0462 (from clone DKFZp564D0462).362   346716.17c g1147782 0 Human myosin-IXb mRNA, complete cds. 363  346716.21c Incyte Unique 364 330776.1 Incyte Unique 365   407999.1cIncyte Unique 366  1719478CB1 g758109 0 Human mRNA for voltage-activatedsodium channel. 367  1719478CD1  g758109 0 Human mRNA forvoltage-activated sodium channel. 368 351157.2 g31139 6.00E−64 HumanEMX1 mRNA. 369   088957CB1 g763428 0 Human mRNA clone with similarity toL-glycerol-3-phosphate:NAD oxidorcductase and albumin gene sc 370   088957CD1 g763428 0 Human mRNA clone with similarity toL-glycerol-3-phosphate:NAD oxidoreductase and albumin gene sc 371980446.1 g2769702 0.088 chondroitin-6-sulfotransferase [Homo sapiens]372 198827.1 g1O17792 0 Human substance P beta-PPT-A mRNA, complete cds.373 1102297.22 g28335 0 Human ACTB mRNA for mutant beta-actin(beta′-actin). 374 215112.1 g4240476 0 Human short chainL-3-hydroxyacyl-CoA dehydrogenase precursor (HADHSC) gene, nuclear geneencod 375 171495.1 g5102577 0 Human mRNA full length insert cDNA cloneEUROIMAGE 345330. 376  242010.43 g5926690 0 Human genomic DNA,chromosome 6p21.3, HLA Class I region, section 2/20. 377  5834958CB1g881474 0 Human pephBGT-1 betaine-GABA transporter mRNA, complete cds.378  5834958CD1  g881474 0 Human pephBGT-1 betaine-GABA transportermRNA, complete cds. 379   335648.1c g36712 0 Human mRNA for tyrosineaminotransferase (TAT) (EC 2.6.1.5). 380 333840.1 g452443 0 Humanglucose-6-phosphatase mRNA, complete cds. 381 480885.2 g2394309 0 Humanhomeobox protein MEIS2 (MEIS2) mRNA, partial cds. 382   998106.8cg174918 5.00E−13 Human Ala-tRNA. 383 400701.4 Incyte Unique 3841100320.4  g1209060 0 Human cytoplasmic dynein light chain 1 (hdlc1)mRNA, complete cds. 385  246727.11 g337456 0 Human ribonucleoprotein(La) mRNA, 3′ end. 386  246727.17 g178686 0 Human La protein mRNA,complete cds. 387   1102322.12c g32466 0 Human hsc70 gene for 71 kd heatshock cognate protein. 388 1102322.18 g313283 0 African green monkeyhsp70 mRNA. 389  2070610CB1 g338696 0 Human thyroxine-binding globulinmRNA, complete cds. 390  2070610CD1  g338696 0 Human thyroxine-bindingglobulin mRNA, complete cds. 391 336733.3 g6049603 0 Human dickkopf-1(DKK-1) mRNA, complete cds. 392 1326902.13 g219909 0 Human mRNA forlipocortin II, complete cds. 393 1326902.6  g219909 0 Human mRNA forlipocortin II, complete cds. 394  013521.16 g37611 0 Human urf-ret mRNA.395 985369.1 g310099 2.00E−36 Rattus norvegicus developmentallyregulated protein mRNA, 396 002455.1 Incyte Unique 397 372647.1 IncyteUnique 398 208075.1 g23915 3.00E−49 Human 7SK RNA gene and flankingregions. 399 209279.1 g2342725 3.6 hypothetical protein [Arabidopsisthaliana] 400 381058.1 g1021027 0 Human CpG island DNA genomic Mse1fragment, clone 181h1, reverse read cpg181h1.rt1c. 401 046977.1 g40285821.00E−12 Human connective tissue growth factor related protein WISP-2(WISP2) mRNA, complete cds.

[0190] TABLE 4 SEQ ID NO: TEMPLATE II START STOP FRAME Pfam ID PfamDescription E-value 1 220060.4 1 441 forward 1 TransthyretinTransthyretin precursor (formerly prealbumin) 8.20E−103 6 3201389CD1 43326 7tm_1 7 transmembrane receptor (rhodopsin family) 4.20E−103 8086390CD1 21 130 SAA_proteins Serum amyloid A protein 3.00E−85 91102322.16 3 803 forward 3 HSP70 Hsp70 protein 2.40E−12 11 1545176CD1 6612 HSP70 Hsp70 protein 0.00E+00 12 978222.4 1 159 forward 1 HLHHelix-loop-helix DNA-binding domain 1.10E−10 15 1720920CD1 55 181laminin_G Laminin G domain 2.00E−25 17 1857017CD1 475 871 HMG-CoA_reHydroxymethylglutaryl-coenzyme A reductase 1.10E−298 19 2114865CD1 46420 serpin Serpins (serine protease inhibitors) 1.60E−216 21 2700132CD127 91 FHA FHA domain 4.30E−21 22 238349.2 379 837 forward 1 SCP SCP-likeextracellular protein 1.40E−34 27 2516070CD1 2 265 ApolipoproteinApolipoprotein A1/A4/E family 2.00E−137 29 167507CD1 266 370 cystatinCystatin domain 3.40E−39 31 3860413CD1 1 61 metalthio Metallothionein2.10E−25 33 3393861CD1 234 484 fibrinogen_C Fibrinogen beta and gammachains, C-terminal 3.00E−179 globular domain 35 2517374CD1 38 183lipocalin Lipocalin/cytosolic fatty-acid binding 2.10E−33 protein family36 030850.7 1 396 forward 1 arf ADP-ribosylation factor family 1.30E−0540 1269631CD1 1651 1735 fn3 Fibronectin type III domain 9.40E−10 401269631CD1 1197 1237 ldl_recept_a Low-density lipoprotein receptordomain class A 2.50E−17 40 1269631CD1 888 931 ldl_recept_b Low-densitylipoprotein receptor repeat class B 2.00E−06 47 476301CD1 28 586transketolase Transketolase 7.20E−124 54 978740.3 1182 1487 forward 3 PHPH domain 5.10E−06 54 978740.3 516 1049 forward 3 RhoGEF RhoGEF domain1.10E−23 58 2797839CD1 300 585 Nol1_Nop2_S NOl1/NOP2/sun family2.80E−157 60 348072.5 860 1411 forward 2 vwa von Willebrand factor typeA domain 8.80E−13 62 085596CD1 17 126 cystatin Cystatin domain 3.10E−2566 3603037CD1 340 364 zf-C2H2 Zinc finger, C2H2 type 5.50E−07 68088564CD1 24 89 IL8 Small cytokines (intecrine/chemokine), 2.50E−10interleukin-8 like 70 407096.2 1111 1953 forward 1 pyr_redox Pyridinenucleotide-disulphide oxidoreductase 7.60E−05 class-I 70 407096.2 5931489 forward 2 pyr_redox Pyridine nucleotide-disulphide oxidoreductase3.20E−06 class-I 70 407096.2 786 1730 forward 3 pyr_redox Pyridinenucleotide-disulphide oxidoreductase 1.70E−09 class-I 71 209265.54 20412250 forward 1 SH3 SH3 domain 1.30E−05 73 701484CD1 8 614 HSP70 Hsp70protein 0.00E+00 74 251859.2 348 632 forward 3 FKBP FKBP-typepeptidyl-prolyl cis-trans isomerases 9.40E−49 76 3766715CD1 170 198 TPRTPR Domain 7.70E−04 83 1434821CD1 30 71 trefoil Trefoil (P-type) domain1.00E−24 84 289671.27 1273 1614 forward 1 GSHPx Glutathione peroxidases4.40E−68 86 1282225CD1 2 127 lipocalin Lipocalin/cytosolic fatty-acidbinding protein 6.90E−25 family 87 263336.57 55 171 forward 1 metalthioMetallothionein 8.20E−06 88 464689.40 443 631 forward 2 cystatinCystatin domain 6.90E−21 91 243794.23 270 434 forward 3 Ribosomal_S1Ribosomal protein S14p/S29e 6.80E−19 98 347055.4 279 1649 forward 3HMG_CoA_sy Hydroxymethylglutaryl-coenzyme A synthase 0.00E+00 99898899.11 661 1266 forward 1 trypsin Trypsin 2.10E−39 99 898899.11 281517 forward 2 kringle Kringle domain 1.50E−50 100 898899.32 1222 1383forward 1 kringle Kringle domain 5.60E−09 100 898899.32 379 609 forward1 PAN PAN domain 1.50E−06 100 898899.32 1367 1543 forward 2 kringleKringle domain 1.10E−07 100 898899.32 2141 2785 forward 2 trypsinTrypsin 4.50E−46 100 898899.32 723 965 forward 3 kringle Kringle domain1.40E−21 102 2047630CD1 206 557 Asn_synthase Asparagine synthase9.00E−261 102 2047630CD1 2 148 GATase_2 Glutamine amidotransferasesclass-II 9.90E−65 103 1039889.8 265 1002 forward 1 actin Actin 2.40E−83103 1039889.8 968 1204 forward 2 actin Actin 5.30E−43 103 1039889.8 12811694 forward 3 actin Actin 4.40E−67 105 1272969CD1 79 391 filamentIntermediate filament proteins 4.30E−157 109 1448817CD1 30 89 IGFBPinsulin-like growth factor binding proteins 2.20E−23 109 1448817CD1 176251 thyroglobulin_(—) Thyroglobulin type-1 repeat 5.50E−40 110 1100769.2262 603 forward 1 Ribosomal_S2 Ribosomal protein S26e 9.20E−75 1101100769.2 663 884 forward 3 Ribosomal_S2 Ribosomal protein S26e 9.80E−30112 225080.16 510 641 forward 3 prenyltrans Prenyltransferase andsqualene oxidase repeat 6.50E−13 113 334851.5 138 452 forward 3 CHCalponin homology (CH) domain 2.00E−25 114 995529.7 46 726 forward 1pkinase Eukaryotic protein kinase domain 6.00E−46 115 995529.8 53 766forward 2 pkinase Eukaryotic protein kinase domain 1.00E−87 115 995529.8795 872 forward 3 pkinase Eukaryotic protein kinase domain 2.70E−07 116201851.1 1634 1750 forward 2 WD40 WD domain, G-beta repeat 1.20E−08 118059509CD1 153 280 TNF TNF (Tumor Necrosis Factor) family 4.00E−15 119481231.14 112 573 forward 1 Apolipoprotein Apolipoprotein A1/A4/E family5.80E−34 124 153825.1 820 951 forward 1 hemopexin Hemopexin 3.80E−14 124153825.1 42 497 forward 3 Peptidase_M 1 Matrixin 5.70E−13 127 1459432CD157 311 7tm_1 7 transmembrane receptor (rhodopsin family) 2.30E−64 130516300CD1 87 174 lectin_c Lectin C-type domain 7.50E−05 132 627856CD1143 239 tRNA_bind Putative tRNA binding domain 5.80E−46 135 232567.4 9021042 forward 2 kazal Kazal-type serine protease inhibitor domain2.30E−17 139 360961.19 1186 1266 forward 1 S-AdoMet_synS-adenosylmethionine synthetase 1.80E−22 139 360961.19 149 604 forward 2S-AdoMet_syn S-adenosylmethionine synthetase 4.00E−87 141 809809CD1 264303 zf-C3HC4 Zinc finger, C3HC4 type (RING finger) 8.10E−06 1432558815CD1 45 511 aldedh Aldehyde dehydrogenase family 3.50E−216 144242010.16 217 2037 forward 1 HSP70 Hsp70 protein 0.00E+00 146 1678695CD16 612 HSP70 Hsp70 protein 0.00E+00 147 988653.1 1295 1369 forward 2zf-C2H2 Zinc finger, C2H2 type 1.00E−06 149 1250434CD1 303 346 PAC PACmotif 1.60E−10 151 442308.1 294 464 forward 3 homeobox Homeobox domain2.70E−27 154 014284CD1 231 458 Peptidase_C1 Papain family cysteineprotease 8.30E−106 160 405844.21 133 498 forward 1 Ephrin Ephrin7.60E−80 161 405844.22 157 573 forward 1 Ephrin Ephrin 1.30E−96 1632705515CD1 158 381 tRNA-synt_1b tRNA synthetases class I (W and Y)1.10E−37 163 2705515CD1 12 68 WHEP-TRS WHEP-TRS domain containingproteins 2.90E−30 165 2023119CD1 39 665 PHO4 Phosphate transporterfamily 0.00E+00 166 1000084.27 152 1423 forward 2 tubulin Tubulin/FtsZfamily 2.40E−279 169 206044.1 248 532 forward 2 serpin Serpins (serineprotease inhibitors) 7.10E−25 170 382906.16 182 226 forward 2transmembrane Transmembrane 4 family 4.40E−04 171 331306.1 967 1029forward 1 7tm_1 7 transmembrane receptor (rhodopsin family) 8.90E−08 171331306.1 312 1001 forward 3 7tm_1 7 transmembrane receptor (rhodopsinfamily) 2.50E−88 172 1094829.20 1365 1559 forward 3 bZIP bZIPtranscription factor 2.90E−19 173 1094829.38 1692 1886 forward 3 bZIPbZIP transcription factor 2.90E−19 175 196623.3 511 984 forward 1 ECHEnoyl-CoA hydratase/isomerase family 3.80E−06 175 196623.3 159 413forward 3 ACBP Acyl CoA binding protein 6.10E−40 176 048488.32 348 2465forward 3 HSP70 Hsp70 protein 2.70E−220 178 2767012CD1 6 68 DnaJ DnaJdomain 1.40E−34 178 2767012CD1 220 346 DnaJ_C DnaJ C terminal region2.50E−07 178 2767012CD1 121 207 DnaJ_CXXCX DnaJ central domain (4repeats) 5.80E−43 180 1651724CD1 40 400 Orn_DAP_Arg Pyridoxal-dependentdecarboxylase 2.30E−202 184 2706645CD1 53 81 efhand EF hand 5.90E−06 1842706645CD1 4 47 S_100 S-100/ICaBP type calcium binding domain 3.60E−23185 474372.7 406 1164 forward 1 pkinase Eukaryotic protein kinase domain3.80E−88 187 3592543CD1 250 314 bZIP bZIP transcription factor 4.90E−22189 048612.13 203 1984 forward 2 PEPCK Phosphoenolpyruvate carboxykinase0.00E+00 190 245259.16 398 955 forward 2 ras Ras family 6.90E−91 192522433CD1 211 308 TGF-beta Transforming growth factor beta like domain6.80E−19 195 2048551CD1 1 61 metalthio Metallothionein 1.80E−24 1981326983.14 518 1768 forward 2 Aa_trans Transmembrane amino acidtransporter protein 9.50E−15 198 1326983.14 518 1768 forward 2 Aa_transTransmembrane amino acid transporter protein 9.50E−15 202 3551330CD1 461 LIM LIM domain containing proteins 2.10E−19 204 1440032CD1 8 614HSP70 Hsp70 protein 0.00E+00 205 1000133.1 199 321 forward 1 ThymosinThymosin beta-4 family 1.90E−21 207 4020439CD1 1 114 Ribosomal_S2Ribosomal protein S26e 4.70E−67 213 021524.9 318 434 forward 3 WD40 WDdomain, G-beta repeat 1.80E−06 215 344553.1 159 1820 forward 3Vitellogenin_(—) Lipoprotein amino terminal region 1.80E−160 216410785.1 72 1535 forward 3 sugar_tr Sugar (and other) transporter2.40E−200 217 237623.6 155 280 forward 2 trefoil Trefoil (P-type) domain2.00E−25 219 1099500.15 466 1116 forward 1 HSP90 Hsp90 protein 1.20E−128219 1099500.15 263 472 forward 2 HSP90 Hsp90 protein 5.50E−41 2191099500.15 102 287 forward 3 HSP90 Hsp90 protein 1.00E−41 220 1099500.181187 1630 forward 2 HSP90 Hsp90 protein 1.70E−113 220 1099500.18 4802609 forward 3 HSP90 Hsp90 protein 0.00E+00 222 2278688CD1 54 441Peptidase_M1 Peptidase family M1 2.90E−234 223 380283.1 111 392 forward3 SCAN SCAN domain 2.80E−11 223 380283.1 2889 2957 forward 3 zf-C2H2Zinc finger, C2H2 type 3.20E−06 232 575983CD1 8 79 ubiquitin Ubiquitinfamily 7.90E−09 235 1989186CD1 447 752 HECT HECT-domain(ubiquitin-transferase). 5.70E−130 235 1989186CD1 289 318 WW WW domain3.00E−16 238 420527.25 924 1871 forward 3 pkinase Eukaryotic proteinkinase domain 5.90E−79 239 998034.3 931 1152 forward 1 transcript_fac2Transcription factor TFIIB repeat 5.80E−19 240 474165.26 244 465 forward1 PWI PWI domain 2.60E−41 242 697785CD1 22 126 Gal-bind_lecti Vertebrategalactoside-binding lectins 2.90E−65 243 346209.3 285 2861 forward 3Myosin_tail Myosin tail 2.00E−181 245 167772CD1 1 61 metalthioMetallothionein 2.20E−23 247 2514988CD1 2 284 ApolipoproteinApolipoprotein A1/A4/E family 9.20E−144 248 481231.16 77 823 forward 2Apolipoprotein Apolipoprotein A1/A4/E family 2.90E−123 249 481231.17 8291599 forward 1 Apolipoprotein Apolipoprotein A1/A4/E family 2.20E−130249 481231.17 216 986 forward 3 Apolipoprotein Apolipoprotein A1/A4/Efamily 1.60E−103 250 1045853.2 955 1713 forward 1 NAD_Gly3P_(—)NAD-dependent glycerol-3-phosphate dehydrogenase 2.00E−11 250 1045853.21889 2413 forward 2 transport_prot Serum albumin family 1.20E−89 251336615.1 86 874 forward 2 Tub Tub family 3.00E−195 254 1081605.3 177 365forward 3 KRAB KRAB box 4.10E−29 254 1081605.3 2649 2717 forward 3zf-C2H2 Zinc finger, C2H2 type 3.90E−08 256 480169.76 337 453 forward 1WD40 WD domain, G-beta repeat 2.80E−07 260 2993696CD1 30 636 HSP70 Hsp70protein 0.00E+00 266 253783.3 976 1185 forward 1 rrm RNA recognitionmotif, (a.k.a. RRM, RBD, or RNP 6.40E−21 domain) 266 253783.3 976 1185forward 1 rrm RNA recognition motif, (a.k.a. RRM, RBD, or RNP 6.40E−21domain) 268 902559.1 733 1191 forward 1 Furin-like Furin-like cysteinerich region 1.70E−97 268 902559.1 358 732 forward 1 Recep_L_dom ReceptorL domain 6.50E−60 268 902559.1 2238 2996 forward 3 pkinase Eukaryoticprotein kinase domain 3.20E−61 272 2757583CD1 1 61 metalthioMetallothionein 1.20E−24 275 1508254CD1 16 463 hexokinase Hexokinase0.00E+00 278 2457215CD1 299 364 rrm RNA recognition motif, (a.k.a. RRM,RBD, or RNP 8.40E−16 domain) 285 1427459CD1 22 60 zf-C3HC4 Zinc finger,C3HC4 type (RING finger) 5.60E−14 288 241291.28 3067 3267 forward 1 FYVEFYVE zinc finger 9.30E−21 291 3993708CD1 2 42 Thymosin Thymosin beta-4family 1.80E−24 292 1000133.12 76 198 forward 1 Thymosin Thymosin beta-4family 1.80E−24 298 898779CD1 136 239 Gal-bind_lecti Vertebrategalactoside-binding lectins 3.80E−50 304 348082.7 686 946 forward 2 PDZPDZ domain (Also known as DHR or GLGF). 1.20E−19 305 1097910.1 53 835forward 2 p450 Cytochrome P450 4.60E−107 311 2253717CD1 48 141 FKBPFKBP-type peptidyl-prolyl cis-trans isomerases 1.40E−27 318 2477616CD111 133 NTF2 Nuclear transport factor 2 (NTF2) domain 5.30E−67 3182477616CD1 342 402 rrm RNA recognition motif, (a.k.a. RRM, RBD, or RNP1.70E−12 domain) 319 360532.1 574 660 forward 1 efhand EF hand 3.00E−08320 360532.9 473 559 forward 2 efhand EF hand 3.00E−08 322 478620.53 9241163 forward 3 rrm RNA recognition motif, (a.k.a. RRM, RBD, or RNP1.10E−17 domain) 322 478620.53 1329 1424 forward 3 zf-RanBP Zn-finger inRan binding protein and others. 1.50E−11 325 474588.21 2263 2460 forward1 rrm RNA recognition motif, (a.k.a. RRM, RBD, or RNP 9.20E−21 domain)325 474588.21 1863 2075 forward 3 rrm RNA recognition motif, (a.k.a.RRM, RBD, or RNP 6.90E−09 domain) 333 4005778CD1 13 169 ferritinFerritins 6.90E−99 334 995575.17 439 1260 forward 1 NAP_familyNucleosome assembly protein (NAP) 8.80E−191 336 863406CD1 15 717 CullinCullin family 2.50E−234 337 413864.17 910 1008 forward 1 ank Ank repeat2.30E−07 338 350106.16 574 1905 forward 1 GLFV_dehydrGlutamate/Leucine/Phenylalanine/Valine dehydrogenase 1.70E−200 341255824.39 568 1317 forward 1 glycolytic_enz Fructose-bisphosphatealdolase class-I 9.60E−192 341 255824.39 276 581 forward 3glycolytic_enz Fructose-bisphosphate aldolase class-I 2.70E−65 3432706606CD1 15 364 glycolytic_enz Fructose-bisphosphate aldolase class-I7.60E−270 345 1039889.26 515 1279 forward 2 actin Actin 3.90E−190 3451039889.26 117 491 forward 3 actin Actin 2.40E−89 346 481480.7 112 348forward 1 ICE_p10 ICE-like protease (caspase) p10 domain 6.40E−41 351331104.2 481 2220 forward 1 PAL Phenylalanine and histidineammonia-lyases 0.00E+00 352 348390.2 108 413 forward 3 actin Actin9.40E−59 357 364726.10 333 647 forward 3 Guanylate_kin Guanylate kinase7.10E−17 358 364726.12 2317 2631 forward 1 Guanylate_kin Guanylatekinase 5.60E−10 358 364726.12 223 483 forward 1 PDZ PDZ domain (Alsoknown as DHR or GLGF). 9.20E−20 360 1505038CD1 54 98 kazal Kazal-typeserine protease inhibitor domain 7.20E−12 367 1719478CD1 1177 1445ion_trans Ion transport protein 2.00E−100 368 351157.2 3 134 forward 3homeobox Homeobox domain 6.60E−13 370 088957CD1 28 202 transport_protSerum albumin family 1.20E−89 373 1102297.22 1354 2481 forward 1 actinActin 1.70E−286 375 171495.1 67 237 forward 1 homeobox Homeobox domain4.10E−34 376 242010.43 2 1267 forward 2 HSP70 Hsp70 protein 5.00E−129378 5834958CD1 36 575 SNF Sodium:neurotransmitter symporter family0.00E+00 384 1100320.4 237 503 forward 3 Dynein_light Dynein light chaintype I 1.10E−62 386 246727.17 469 678 forward 1 rrm RNA recognitionmotif, (a.k.a. RRM, RBD, or RNP 1.00E−13 domain) 388 1102322.18 5 751forward 2 HSP70 Hsp70 protein 3.80E−05 390 2070610CD1 39 412 serpinSerpins (serine protease inhibitors) 2.70E−194 392 1326902.13 270 473forward 3 annexin Annexin 5.20E−18 393 1326902.6 919 1122 forward 1annexin Annexin 5.20E−18 393 1326902.6 459 662 forward 3 annexin Annexin1.10E−24 394 013521.16 486 734 forward 3 PH PH domain 1.50E−09

[0191] TABLE 5 SEQ TEMPLATE HIT ID NO: II START STOP FRAME TYPE 63201389CD1 26 52 TM 6 3201389CD1 185 210 TM 6 3201389CD1 145 171 SP 91102322.16 127 219 forward 1 SP 9 1102322.16 313 396 forward 1 SP 12978222.4 533 625 forward 2 SP 13 978222.5 660 737 forward 3 TM 151720920CD1 2220 2246 TM 15 1720920CD1 2222 2248 SP 15 1720920CD1 1 30 SP17 1857017CD1 10 36 TM 33 3393861CD1 1 29 SP 35 2517374CD1 1 34 SP 38237416.14 570 665 forward 3 SP 38 237416.14 863 940 forward 2 TM 401269631CD1 1 28 SP 50 2989375CD1 23 49 SP 54 978740.3 3103 3186 forward1 TM 54 978740.3 652 741 forward 1 SP 55 400197.1 244 321 forward 1 TM60 348072.5 243 323 forward 3 SP 60 348072.5 780 881 forward 3 SP 60348072.5 132 221 forward 3 SP 60 348072.5 1659 1751 forward 3 SP 60348072.5 10 99 forward 1 SP 68 088564CD1 1 26 SP 69 040429.1 656 739forward 2 TM 69 040429.1 93 179 forward 3 SP 70 407096.2 1083 1157forward 3 TM 70 407096.2 1099 1179 forward 1 SP 83 1434821CD1 1 26 SP 84289671.27 1132 1221 forward 1 SP 84 289671.27 1298 1375 forward 2 SP 88464689.40 281 361 forward 2 SP 89 155943.1 964 1047 forward 1 SP 89155943.1 995 1069 forward 2 TM 95 1273641CD1 136 161 SP 98 347055.4 17691864 forward 2 SP 100 898899.32 242 337 forward 2 SP 109 1448817CD1 1 31SP 111 332521.1 397 483 forward 1 SP 112 225080.16 2387 2488 forward 2SP 114 995529.7 275 358 forward 2 SP 115 995529.8 285 368 forward 3 SP115 995529.8 1605 1688 forward 3 TM 116 201851.1 3954 4034 forward 3 TM118 059509CD1 3 32 SP 127 1459432CD1 41 66 TM 130 516300CD1 1 28 SP 147988653.1 1080 1166 forward 3 SP 147 988653.1 3422 3502 forward 2 TM 150236196.3 563 643 forward 2 TM 150 236196.3 754 834 forward 1 SP 150236196.3 851 928 forward 2 TM 154 014284CD1 1 28 SP 159 978276.8 20412115 forward 1 TM 159 978276.8 2041 2115 forward 1 TM 160 405844.21 559651 forward 1 SP 161 405844.22 649 741 forward 1 SP 165 2023119CD1 23 50TM 165 2023119CD1 562 587 TM 166 1000084.27 4622 4705 forward 2 SP 1661000084.27 309 410 forward 3 SP 166 1000084.27 1089 1169 forward 3 SP166 1000084.27 4170 4259 forward 3 SP 166 1000084.27 4040 4123 forward 2SP 166 1000084.27 4138 4227 forward 1 SP 167 220134.1 2246 2326 forward2 TM 168 216331.1 1465 1551 forward 1 TM 170 382906.16 155 238 forward 2SP 171 331306.1 273 350 forward 3 TM 171 331306.1 2517 2594 forward 3 TM171 331306.1 897 974 forward 3 TM 171 331306.1 576 659 forward 3 TM 1721094829.20 1156 1242 forward 1 SP 172 1094829.20 673 756 forward 1 SP173 1094829.38 1468 1554 forward 1 SP 173 1094829.38 985 1068 forward 1SP 174 1135580.4 4037 4120 forward 2 TM 174 1135580.4 4599 4685 forward3 SP 174 1135580.4 4492 4581 forward 1 SP 174 1135580.4 3367 3453forward 1 SP 174 1135580.4 1701 1790 forward 3 SP 174 1135580.4 41034183 forward 2 SP 175 196623.3 659 739 forward 2 SP 176 048488.32 27582835 forward 1 TM 182 461707.40 185 268 forward 2 SP 185 474372.7 21062198 forward 3 SP 185 474372.7 2084 2164 forward 2 TM 189 048612.13 663743 forward 3 SP 192 522433CD1 1 29 SP 198 1326983.14 4115 4198 forward2 TM 198 1326983.14 2343 2423 forward 3 TM 198 1326983.14 114 197forward 3 TM 198 1326983.14 2467 2550 forward 1 TM 198 1326983.14 15471624 forward 2 TM 198 1326983.14 1406 1483 forward 2 TM 198 1326983.144115 4198 forward 2 TM 198 1326983.14 2343 2423 forward 3 TM 1981326983.14 114 197 forward 3 TM 198 1326983.14 2467 2550 forward 1 TM198 1326983.14 1547 1624 forward 2 TM 198 1326983.14 1406 1483 forward 2TM 200 2120743CD1 295 323 TM 200 2120743CD1 189 219 SP 200 2120743CD1344 374 SP 200 2120743CD1 87 113 SP 211 1097380.1 864 962 forward 3 SP211 1097380.1 1360 1440 forward 1 TM 214 253987.16 512 592 forward 2 TM215 344553.1 3343 3420 forward 1 TM 216 410785.1 2055 2141 forward 3 TM216 410785.1 4411 4494 forward 1 TM 216 410785.1 997 1080 forward 1 SP216 410785.1 1383 1469 forward 3 TM 216 410785.1 4554 4637 forward 3 TM217 237623.6 24 104 forward 3 SP 219 1099500.15 10 102 forward 1 TM 2222278688CD1 1 39 SP 223 380283.1 6996 7079 forward 3 TM 223 380283.1 73153 forward 1 SP 223 380283.1 3502 3591 forward 1 SP 223 380283.1 79398019 forward 1 TM 223 380283.1 6383 6460 forward 2 TM 223 380283.1 64796562 forward 2 TM 223 380283.1 6083 6175 forward 2 SP 228 3478236CD1 126 SP 228 3478236CD1 191 217 SP 229 147541.17 4089 4178 forward 3 SP 233413268.6 4424 4513 forward 2 SP 233 413268.6 3689 3772 forward 2 SP 233413268.6 893 979 forward 2 SP 238 420527.25 660 737 forward 3 TM 238420527.25 662 742 forward 2 TM 240 474165.26 2961 3074 forward 3 SP 240474165.26 3015 3098 forward 3 TM 243 346209.3 3564 3650 forward 3 SP 249481231.17 1760 1846 forward 2 SP 250 1045853.2 1238 1324 forward 2 SP253 085282.1 339 422 forward 3 TM 258 2636043CD1 117 143 TM 262240518.34 1591 1701 forward 1 SP 266 253783.3 1181 1264 forward 2 SP 266253783.3 1181 1264 forward 2 SP 268 902559.1 4378 4464 forward 1 SP 268902559.1 512 607 forward 2 SP 276 474691.3 1030 1107 forward 1 SP 276474691.3 3859 3945 forward 1 TM 276 474691.3 3957 4040 forward 3 TM 2831040190.3 81 164 forward 3 SP 287 1095604.1 182 262 forward 2 SP 288241291.28 10604 10684 forward 2 SP 288 241291.28 73 153 forward 1 SP 288241291.28 4075 4176 forward 1 SP 288 241291.28 11296 11373 forward 1 TM288 241291.28 10088 10168 forward 2 SP 288 241291.28 10841 10921 forward2 TM 288 241291.28 3228 3311 forward 3 SP 288 241291.28 655 738 forward1 SP 294 400253.5 1917 1994 forward 3 SP 294 400253.5 748 828 forward 1SP 294 400253.5 1063 1152 forward 1 SP 294 400253.5 1963 2040 forward 1SP 294 400253.5 213 293 forward 3 SP 305 1097910.1 204 284 forward 3 SP305 1097910.1 582 662 forward 3 SP 306 246841.1 2036 2137 forward 2 SP307 351241.1 139 219 forward 1 TM 311 2253717CD1 1 27 SP 315 232818.15204 290 forward 3 SP 315 232818.15 782 862 forward 2 TM 322 478620.53306 386 forward 3 SP 322 478620.53 227 313 forward 2 SP 322 478620.531135 1227 forward 1 SP 325 474588.21 1315 1392 forward 1 TM 328 347796.72467 2550 forward 1 TM 334 995575.17 1691 1771 forward 2 SP 334995575.17 1641 1727 forward 3 TM 334 995575.17 3283 3363 forward 1 TM337 413864.17 1178 1258 forward 2 TM 337 413864.17 1159 1239 forward 1TM 350 235447.5 5478 5558 forward 3 TM 351 331104.2 2656 2754 forward 1SP 356 480375.28 54 134 forward 3 TM 356 480375.28 50 130 forward 2 TM356 480375.28 54 134 forward 3 TM 356 480375.28 50 130 forward 2 TM 357364726.10 1380 1466 forward 3 SP 358 364726.12 4106 4183 forward 2 TM361 903508.12 2552 2632 forward 2 TM 363 346716.21c 529 609 forward 1 SP367 1719478CD1 1734 1760 TM 367 1719478CD1 1631 1656 TM 367 1719478CD1380 407 TM 367 1719478CD1 1627 1653 SP 367 1719478CD1 939 967 SP 371980446.1 353 427 forward 2 TM 373 1102297.22 173 256 forward 2 SP 3731102297.22 1838 1924 forward 2 SP 374 215112.1 383 466 forward 2 TM 375171495.1 1008 1097 forward 3 TM 378 5834958CD1 408 435 TM 378 5834958CD1488 518 SP 378 5834958CD1 373 402 SP 380 333840.1 1873 1950 forward 1 TM380 333840.1 2180 2269 forward 2 SP 380 333840.1 1818 1901 forward 3 SP386 246727.17 2262 2348 forward 3 SP 388 1102322.18 155 247 forward 2 SP397 372647.1 215 295 forward 2 TM 399 209279.1 661 741 forward 1 SP

[0192] TABLE 6 SEQ ID TEMPLATE CLONE NO: I ID START STOP 1 220060.426474 1 274 2 016238.1 60123 1 218 3 1266683.1  63038 1 212 4  129384.1c 72713 225 440 5  3201389CB1 85606 1 2537 7   086390CB1 8639023 647 9 1102322.16 118501 280 852 10  1545176CB1 118501 36 2295 12978222.4 121785 764 1167 13 978222.5 121785 92 636 14  1720920CB1 13607371 7699 16  1857017CB1 160822 334 4843 16  1857017CB1 3493710 334 484318  2114865CB1 167081 369 1949 20  2700132CB1 172023 70 10502 20 2700132CB1 2470485 70 10502 22 238349.2 211389 4294 4448 23   238349.4c211389 1 110 24   402917.3c 237027 428 858 25 406330.1 259054 482 117926  2516070CB1 271299 757 1693 26  2516070CB1 2517386 757 1693 28  167507CB1 279249 1 1656 30  3860413CB1 279898 1 617 30  3860413CB13121871 1 617 32  3393861CB1 280932 28 1656 34  2517374CB1 293477 16 86836 030850.7 311346 1 483 37   237416.12c 318486 1 567 38  237416.14318486 93 616 39  1269631CB1 341884 118 6985 41   961189CB1 348143 252192 43 246946.1 388964 0 394 44 017958.1 389362 1 259 45 985556.1407032 906 1234 46   476301CB1 408886 1 2523 48 996427.2 419492 801 245849  2989375CB1 437481 1 902 51 236359.2 442723 112 618 52   011112.1C443991 12 342 53 198268.1 450856 297 854 54 978740.3 452321 2764 3535 55400197.1 454839 1 1025 56   235687.5c 459372 −27 410 57  2797839CB1460779 1 2650 59 978690.6 462069 164 864 60 348072.5 480791 1960 2765 61  085596CB1 481402 119 2070 63   103917CB1 510056 39 1674 65  3603037CB1511448 1 2979 67   088564CB1 560115 1 823 69 040429.1 604019 736 1087 70407096.2 630625 2268 3868 71  209265.54 669498 2155 2752 72   701484CB1701484 −188 2308 74 251859.2 758192 654 3262 75  3766715CB1 773154 16665251 77  2049950CB1 818192 347 3779 79   231588.6c 818192 1 557 80152298.2 872017 84 834 81 199507.1 891322 1 342 82  1434821CB1 963536−298 620 84  289671.27 970905 2307 2723 85  1282225CB1 990375 130 657 87 263336.57 1213932 4 324 88  464689.40 1259841 1 897 89 155943.1 1272483339 840 90   243794.19c 1306814 834 1050 91  243794.23 1306814 284 52292   159309CB1 1308112 21 3061 94  1273641CB1 1315663 127 1425 96403717.1 1316801 1 773 97 047593.1 1326255 1 794 98 347055.4 13688343159 3550 99  898899.11 1379063 1046 1377 100  898899.32 1379063 20522524 101  2047630CB1 1381654 180 2123 103 1039889.8  1395143 609 994 104 1272969CB1 1435374 2984 4434 106   282397.85c 1441245 2665 6228 107 282397.94 1441245 1 622 108  1448817CB1 1448718 15 1535 110 1100769.2 1454436 35 697 111 332521.1 1457424 871 1424 112  225080.16 1457718 40474330 113 334851.5 1464613 757 1127 114 995529.7 1468660 445 843 115995529.8 1468660 938 1169 116 201851.1 1482116 3045 3958 117   059509CB11495382 16 1623 119  481231.14 1500245 1 406 120   280276CB1 1511658 1122332 122  4675668CB1 1519431 17 1723 124 153825.1 1519683 560 1056 125  403484.2c 1522880 1695 2180 126  1459432CB1 1522880 1 2144 1281096583.1  1530595 233 424 129   516300CB1 1559665 1 763 131   627856CB11559756 550 1997 133  1823159CB1 1560906 1 3471 135 232567.4 1577614 5131142 136 218419.1 1616783 1 184 137  1630551CB1 1619292 2 1229 139 360961.19 1619980 1208 1470 140   809809CB1 1623214 1 2116 142 2558815CB1 1630990 −4 2431 144  242010.16 1696224 1767 2352 145 1678695CB1 1696224 −761 1690 147 988653.1 1705208 1702 2382 148 1250434CB1 1711151 46 3277 150 236196.3 1732221 1 524 151 442308.11756875 1 375 152 060957.1 1786554 1 597 153   014284CB1 1822716 2 1900155 1095192.1  1833362 247 684 156  233003.20 1834236 1 552 157 1911808CB1 1834236 88 3722 159 978276.8 1838114 3037 3497 160 405844.21 1845046 341 938 161  405844.22 1845046 925 1484 162 2705515CB1 1846209 1 2256 164  2023119CB1 1846463 34 3324 1661000084.27 1861456 1583 1991 166 1000084.27 3679667 1646 2138 167220134.1 1867614 477 2949 168 216331.1 1869130 1226 1976 169 206044.11871340 347 580 170  382906.16 1874037 54 505 171 331306.1 1874307 15762007 172 1094829.20 1890576 1268 1652 173 1094829.38 1890576 566 1023174 1135580.4  1890791 3964 5687 175 196623.3 1920215 1299 1746 176 048488.32 1922468 2741 3572 177  2767012CB1 1926883 17 1485 179 1651724CB1 1930235 41 2059 181 206397.1 1956982 1 237 182  461707.401958226 353 701 183  2706645CB1 1963081 13 975 185 474372.7 1966517 20372539 186  3592543CB1 1969563 1 2198 188   048612.12c 1975268 872 1420189  048612.13 1975268 2418 2666 190  245259.16 1998269 1787 2319 191  522433CB1 2042056 15 1251 193 1040667.43 2046717 1 372 194  2048551CB12048551 1 558 196  1969731CB1 2055569 3 3038 198 1326983.14 2055867 40294749 199  2120743CB1 2120743 1 3934 201  3551330CB1 2121863 334 770 203 1440032CB1 2123516 622 2962 205 1000133.1  2132285 137 609 206 4020439CB1 2132774 260 700 208  2507087CB1 2160794 1 4241 210 239996.12195427 127 589 211 1097380.1  2201708 43 967 212   021524.2c 22087803082 3404 213 021524.9 2208780 1272 1527 214  253987.16 2232658 1 360215 344553.1 2234853 2584 3171 216 410785.1 2241825 4508 4883 217237623.6 2242817 1 451 218 076047.1 2252107 1 392 219 1099500.15 22739441107 1756 220 1099500.18 2273944 2360 2777 221  2278688CB1 2278688 12335389 223 380283.1 2293496 7546 7928 224  1720847CB1 2311213 855 1844 226  333776.1c 2343348 126 201 227  3478236CB1 2352645 1 1278 229 147541.17 2360580 1850 3484 230   331120.16c 2365335 4150 4601 231  575983CB1 2382192 1 798 233 413268.6 2382195 2182 4148 234  1989186CB12383269 904 3033 236   337448.1c 2394990 1 308 237  228304.19 2399162636 1144 238  420527.25 2446289 248 2143 239 998034.3 2448149 377 3629240  474165.26 2453558 105 560 241   697785CB1 2495131 233 770 243346209.3 2511277 3331 3758 244   167772CB1 2513883 505 974 246 2514988CB1 2514988 199 1492 248  481231.16 2516070 57 461 249 481231.17 2516070 205 1661 249  481231.17 2516104 819 1661 249 481231.17 2516261 197 1659 249  481231.17 2516448 1395 1698 2501045853.2  2517254 1874 3884 250 1045853.2  5398014 1874 3898 251336615.1 2520894 1088 1325 252 1328423.2  2527879 423 938 253 085282.12545486 83 487 254 1081605.3  2550767 3196 3739 255 1053517.1  2579218 1233 256  480169.76 2607921 716 2565 257  2636043CB1 2636043 98 1101 259 2993696CB1 2641522 −8 2532 261  240518.21 2660756 1 333 262  240518.342660756 534 1026 263   001322.4c 2663164 1069 3206 264 350502.3 267523239 440 265   350502.4c 2675232 547 1016 266 253783.3 2695371 993 1843267 085119.1 2708055 577 869 268 902559.1 2740665 5148 5635 269 4113161CB1 2756333 108 2295 271  2757583CB1 2757583 268 709 273198317.1 2765271 29 881 274  1508254CB1 2769888 1363 4652 276 474691.32813255 820 1466 277  2457215CB1 2820337 1 3437 279   201395.4c 28220274780 5689 280  233189.21 2825358 85 565 281   196606.6c 2830828 1 566282   196606.8c 2830828 113 696 283 1040190.3  2831490 38 1110 284 1427459CB1 2860918 −28 1364 286   480453.16c 2879068 2710 3067 2871095604.1  2884613 3 282 288  241291.28 2890336 2125 2463 289 230611.12891601 1 64 290  3993708CB1 2899419 59 633 292 1000133.12 2899419 13307 293   400253.17c 2912637 4051 4601 294 400253.5 2912637 238 742 295  030882CB1 2912830 67 443 297   898779CB1 2921194 294 1408 299 3727408CB1 2921991 4 532 301   984236.1c 2925373 47 494 302   984236.2c2925373 223 494 303 348082.5 2929484 193 582 304 348082.7 2929484 516980 305 1097910.1  2933775 389 886 306 246841.1 2953987 2907 3189 307351241.1 2955163 312 757 308  2790762CB1 2956444 158 1221 310 2253717CB1 2957205 103 815 312  2655184CB1 2991027 401 1496 314  363000.9c 2991027 1014 1447 315  232818.15 2992044 1069 1721 316 347781.10 2999855 576 937 317  2477616CB1 2999855 1 2835 319 360532.13026540 210 800 320 360532.9 3026540 79 1158 321 110245.1 3028719 1 396322  478620.53 3038508 1447 1779 323  1813444CB1 3038508 7 1694 325 474588.21 3070625 1761 2181 326 407838.1 3074113 234 997 327  994387.193084204 1 509 328 347796.7 3108506 395 687 329   406498.4c 3109384 112525 330  3346307CB1 3120209 2 1747 332  4005778CB1 3121380 208 1220 334 995575.17 3123731 2033 2944 335   863406CB1 3128810 62 4366 337 413864.17 3129338 1 1603 338  350106.16 3136857 1045 1577 339 399785.13158828 199 627 340  010498.19 3170010 3434 4175 341  255824.39 3208425258 755 342  2706606CB1 3208425 347 1869 344 118006.1 3222802 1 162 3451039889.26 3225977 64 1971 346 481480.7 3240708 1 392 347   662575CB13272165 17 1864 349 027619.3 3284411 5 813 350 235447.5 3345528 82748706 351 331104.2 3380034 2256 3067 352 348390.2 3381870 50 205 353127004.1 3407653 1 640 354 026190.1 3427373 970 1345 355 250330.13472927 1 554 356  480375.28 3493381 100 548 357  364726.10 3494714 1498 358  364726.12 3494714 3939 4473 359  1505038CB1 3606046 7 3701 361 903508.12 3715059 1589 2966 362   346716.17c 3792988 6200 6704 363  346716.21c 3792988 55 705 364 330776.1 3815422 2049 2357 365  407999.1c 4019706 1 368 366  1719478CB1 4066764 1 6348 368 351157.24070979 59 653 369   088957CB1 4087621 1888 4200 369   088957CB1 53987011888 4200 371 980446.1 4091186 1 801 372 198827.1 4092112 90 1147 3731102297.22 4107126 1584 1682 374 215112.1 4110976 1 522 375 171495.14203937 51 1219 376  242010.43 4246966 150 335 377  5834958CB1 4254855 12919 379   335648.1c 4284384 33 430 380 333840.1 4287327 1166 1659 381480885.2 4403805 190 2066 382   998106.8c 4508879 15 869 383 400701.44549259 1 449 384 1100320.4  4556538 14 796 385  246727.11 4715924 272642 386  246727.17 4715924 1249 1618 387   1102322.12c 4721130 207 672388 1102322.18 4721130 844 1068 389  2070610CB1 4795635 249 1680 391336733.3 5047895 1 420 392 1326902.13 5077219 105 580 393 1326902.6 5077219 983 1443 394  013521.16 5093071 312 767 395 985369.1 5102731 3371131 396 002455.1 5266015 670 1134 397 372647.1 5266376 81 792 398208075.1 5293028 417 737 399 209279.1 5399371 2090 2521 400 381058.15512044 1 517 401 046977.1 5541949 1 308

[0193] TABLE 7 SEQ ID Template NO: ID Tissue Distribution 1 220060.4Liver - 35%, Sense Organs - 28%, Nervous System - 14% 3 1266683.1 Embryonic Structures - 100% 4   129384.1c Skin - 64%, RespiratorySystem - 14%, Hemic and Immune System - 14% 9 1102322.16 Skin - 12%,Sense Organs - 11% 12 978222.4 Germ Cells - 42%, Unclassified/Mixed -15%, Musculoskeletal System - 10%, Female Genitalia - 10% 13 978222.5Connective Tissue - 18%, Male Genilalia - 18%, Musculoskeletal System -15% 22 238349.2 Embryonic Structures - 17% 23   238349.4c Hemic andImmune System - 100% 24   402917.3c Digestive System - 42%, UrinaryTract - 40% 25 406330.1 Germ Cells - 64%, Nervous System - 36% 37  237416.12c Unclassified/Mixed - 93% 38  237416.14 Exocrine Glands -17%, Liver - 16%, Female Genitalia - 14% 43 246946.1 Female Genitalia -86%, Hemic and Immune System - 10% 45 985556.1 Hemic and Immune System -29%, Respiratory System - 13% 48 996427.2 Hemic and Immune System - 19%,Exocrine Glands - 13%, Respiratory System - 12% 51 236359.2 ConnectiveTissue - 54%, Hemic and Immune System - 46% 53 198268.1 Hemic and ImmuneSystem - 82%, Male Genitalia - 18% 54 978740.3 Sense Organs - 14%, GermCells - 11% 55 400197.1 Skin - 37%, Pancreas - 13%, EmbryonicStructures - 12% 56   235687.5c Germ Cells - 44%, Skin - 23%,Unclassified/Mixed - 16% 59 978690.6 Unclassified/Mixed - 33%, NervousSystem - 21%, Respiratory System - 19% 60 348072.5 Liver - 90% 70407096.2 Connective Tissue - 15% 71  209265.54 Germ Cells - 27%,Musculoskeletal System - 11% 79   231588.6c Respiratory System - 25%,Female Genitalia - 25%, Nervous System - 17%, Digestive System - 17%,Hemic and Immune System - 17% 80 152298.2 Respiratory System - 60%,Digestive System - 40% 81 199507.1 Nervous System - 50%, DigestiveSystem - 50% 84  289671.27 Sense Organs - 26%, Urinary Tract - 19% 87 263336.57 Liver - 23%, Urinary Tract - 17%, Hemic and Immune System -17% 88  464689.40 Female Genitalia - 13%, Liver - 11% 89 155943.1Unclassified/Mixed - 33%, Germ Cells - 30% 90   243794.19cStomatognathic System - 14% 96 403717.1 Unclassified/Mixed - 44%,Embryonic Structures - 21%, Urinary Tract - 19% 98 347055.4 Skin- 15%,Liver- 12% 99  898899.11 Liver - 41%, Respiratory System - 14%,Pancreas - 12% 100  898899.32 Liver - 62%, Urinary Tract - 12% 106  282397.85c Embryonic Structures - 11% 107  282397.94 EndocrineSystem - 71%, Hemic and Immune System - 29% 110 1100769.2  Pancreas -10% 111 332521.1 Unclassified/Mixed - 19%, Embryonic Structures - 18%,Musculoskeletal System - 12% 112  225080.16 Skin - 18% 113 334851.5Liver - 16%, Exocrine Glands - 12%, Digestive System - 11% 114 995529.7Pancreas - 27%, Hemic and Immune System - 23%, Exocrine Glands - 14% 115995529.8 Unclassified/Mixed - 24%, Hemic and Immune System - 15% 116201851.1 Sense Organs - 21%, Unclassified/Mixed - 11%, Nervous System -11% 119  481231.14 Liver - 84%, Digestive System - 12% 124 153825.1Embryonic Structures - 43%, Connective Tissue - 16%,Unclassified/Mixed - 12% 125   403484.2c Germ Cells - 83% 128 1096583.1 Pancreas - 42%, Unclassified/Mixed - 42%, Cardiovascular System - 17%135 232567.4 Skin - 29%, Germ Cells - 22% 136 218419.1Unclassified/Mixed - 42%, Connective Tissue - 29%, Nervous System - 17%139  360961.19 Connective Tissue - 13%, Endocrine System - 13%, Skin -11% 144  242010.16 Nervous System - 18%, Musculoskeletal System - 16%147 988653.1 Connective Tissue - 12%, Exocrine Glands - 12% 150 236196.3Endocrine System - 15%, Musculoskeletal System - 14%, Liver - 10% 151442308.1 Endocrine System - 78%, Nervous System - 22% 155 1095192.1 Nervous System - 100% 156  233003.20 Digestive System - 67%, NervousSystem - 33% 159 978276.8 Sense Organs - 12%, Unclassified/Mixed - 11%160  405844.21 Embryonic Structures - 18%, Liver - 16%, ExocrineGlands - 11% 161  405844.22 Embryonic Structures - 11% 167 220134.1Skin - 22%, Liver- 14% 169 206044.1 Skin - 81%, Unclassified/Mixed - 19%170  382906.16 Skin - 35%, Pancreas - 25%, Hemic and Immune System - 13%171 331306.1 Hemic and Immune System - 25%, Unclassified/Mixed - 13%,Respiratory System - 13% 172 1094829.20 Musculoskeletal System - 10% 1731094829.38 Stomatognathic System - 11% 174 1135580.4  Nervous System -22%, Unclassified/Mixed - 15%, Connective Tissue - 11% 181 206397.1Connective Tissue - 100% 182  461707.40 Liver - 27%, Sense Organs - 26%185 474372.7 Hemic and Immune System - 15% 190  245259.16 UrinaryTract - 12%, Germ Cells - 11% 193 1040667.43 Hemic and Immune System -100% 198 1326983.14 Liver - 10% 205 1000133.1  Stomatognathic System -13%, Cardiovascular System - 12% 210 239996.1 Skin - 45%, ConnectiveTissue - 23%, Hemic and Immune System - 19% 211 1097380.1  SenseOrgans - 14%, Embryonic Structures - 11% 214  253987.16 Urinary Tract -27%, Cardiovascular System - 18%, Musculoskeletal System - 14% 215344553.1 Digestive System - 38%, Liver - 19%, Pancreas - 18% 216410785.1 Liver - 53%, Hemic and Immune System - 14%, Urinary Tract - 12%217 237623.6 Digestive System - 38%, Pancreas - 19%, RespiratorySystem - 11% 219 1099500.15 Stomatognathic System - 11% 220 1099500.18Nervous System - 11% 223 380283.1 Embryonic Structures - 31%, EndocrineSystem - 13% 226   333776.1c Hemic and Immune System - 71%, MaleGenitalia - 29% 229  147541.17 Sense Organs - 12% 230   331120.16cLiver - 13%, Germ Cells - 12%, Unclassified/Mixed - 11% 233 413268.6Stomatognathic System - 11% 236   337448.1c Unclassified/Mixed - 49%,Germ Cells - 23%, Male Genitalia - 14% 237  228304.19 Liver - 42%,Unclassified/Mixed - 10% 238  420527.25 Sense Organs - 12% 239 998034.3Germ Cells - 23% 243 346209.3 Digestive System - 24%, Pancreas - 12% 248 481231.16 Liver - 83%, Digestive System - 12% 249  481231.17 Liver -70%, Digestive System - 14% 250 1045853.2  Liver - 93% 251 336615.1Sense Organs - 57%, Endocrine System - 15%, Unclassified/Mixed - 11% 2521328423.2  Endocrine System - 17%, Embryonic Structures - 11% 2541081605.3  Unclassified/Mixed - 26%, Endocrine System - 16%, MaleGenitalia - 13% 255 1053517.1  Urinary Tract- 100% 261  240518.21Liver - 26%, Respiratory System - 19%, Connective Tissue - 17% 262 240518.34 Pancreas - 10% 264 350502.3 Connective Tissue - 44%,Cardiovascular System - 25%, Urinary Tract - 25% 265   350502.4cExocrine Glands - 28%, Urinary Tract - 28%, Cardiovascular System - 14%266 253783.3 Male Genitalia - 30%, Urinary Tract - 27%, Nervous System -24% 268 902559.1 Digestive System - 12%, Exocrine Glands - 11%, UrinaryTract - 10% 273 198317.1 Musculoskeletal System - 16%, Exocrine Glands -15%, Embryonic Structures - 12%, Unclassified/Mixed - 12% 276 474691.3Germ Cells - 14% 279   201395.4c Nervous System - 38%, EndocrineSystem - 14% 280  233189.21 Liver - 30% 281   196606.6c Hemic and ImmuneSystem - 100% 282   196606.8c Sense Organs - 11%, Connective Tissue -11% 283 1040190.3  Hemic and Immune System - 37%, Germ Cells - 13% 286  480453.16c Urinary Tract - 10% 287 1095604.1  Skin - 28%, EmbryonicStructures - 19%, Endocrine System - 14% 289 230611.1 RespiratorySystem - 60%, Hemic and Immune System - 40% 292 1000133.12Cardiovascular System - 15% 293   400253.17c Germ Cells - 31% 294400253.5 Liver - 41%, Urinary Tract - 19%, Exocrine Glands - 19% 301  984236.1c Digestive System - 35%, Liver - 30%, Female Genitalia - 14%302   984236.2c Digestive System - 72%, Exocrine Glands - 22% 303348082.5 Connective Tissue - 36%, Germ Cells - 19% 304 348082.7Embryonic Structures - 38%, Skin - 23%, Digestive System - 10% 3051097910.1  Liver - 48%, Male Genitalia - 20%, Endocrine System - 11% 306246841.1 Sense Organs - 30% 307 351241.1 Urinary Tract - 36%, Hemic andImmune System - 36%, Musculoskeletal System - 27% 315  232818.15 Skin -12% 316  347781.10 Skin - 20% 319 360532.1 Stomatognathic System - 67%,Musculoskeletal System - 16%, Cardiovascular System - 12% 320 360532.9Musculoskeletal System - 49%, Cardiovascular System - 22%, SenseOrgans - 11% 321 110245.1 Cardiovascular System - 67%, Hemic and ImmuneSystem - 33% 325  474588.21 Female Genitalia - 17%, Respiratory System -15%, Embryonic Structures - 13% 326 407838.1 Musculoskeletal System -60%, Respiratory System - 30%, Nervous System - 10% 327  994387.19Female Genitalia - 75%, Nervous System - 25% 328 347796.7 StomatognathicSystem - 13% 329   406498.4c Sense Organs - 75%, Unclassified/Mixed -14% 334  995575.17 Sense Organs - 14% 337  413864.17 Liver - 18%,Respiratory System - 12%, Exocrine Glands - 11% 339 399785.1 Pancreas -31%, Unclassified/Mixed - 31%, Male Genitalia - 16% 341  255824.39Stomatognathic System - 15%, Musculoskeletal System - 13% 344 118006.1Digestive System - 100% 346 481480.7 Digestive System - 100% 350235447.5 Embryonic Structures - 11%, Liver - 11% 351 331104.2 Liver -64%, Hemic and Immune System - 10% 352 348390.2 Digestive System - 46%,Female Genitalia - 21%, Male Genitalia - 20% 353 127004.1 Germ Cells -84% 355 250330.1 Hemic and Immune System - 63%, Respiratory System -38%; 356  480375.28 Musculoskeletal System - 46%, Endocrine System -38%, Male Genitalia - 15% 357  364726.10 Sense Organs - 39% 358 364726.12 Sense Organs - 15%, Unclassified/Mixed - 14% 361  903508.12Embryonic Structures - 35%, Germ Cells - 15%, Liver - 14% 362  346716.17c Unclassified/Mixed - 23%, Germ Cells - 11%, Hemic andImmune System - 10% 363   346716.21c Cardiovascular System - 18%,Nervous System - 18%, Endocrine System - 13%, Male Genitalia - 13% 364330776.1 Sense Organs - 17%, Connective Tissue - 15% 365   407999.1cNervous System - 100% 368 351157.2 Urinary Tract - 80%, Hemic and ImmuneSystem - 20% 371 980446.1 Embryonic Structures - 31%, Nervous System -16%, Connective Tissue - 11%, Male Genitalia - 11% 372 198827.1Connective Tissue - 25%, Nervous System - 17%, Exocrine Glands - 11% 374215112.1 Male Genitalia - 83%, Nervous System - 17% 375 171495.1Unclassified/Mixed - 43%, Cardiovascular System - 18%, RespiratorySystem - 14% 376  242010.43 Musculoskeletal System - 21%, NervousSystem - 20% 379   335648.1c Liver - 72%, Exocrine Glands - 18% 380333840.1 Liver - 71%, Urinary Tract - 20% 381 480885.2 ConnectiveTissue - 14%, Male Genitalia - 14% 382   998106.8c Unclassified/Mixed -36%, Respiratory System - 26% 383 400701.4 Nervous System - 43%,Endocrine System - 36%, Female Genitalia - 21% 384 1100320.4  NervousSystem - 10%, Skin - 10%, Respiratory System - 10%, Endocrine System -10% 385  246727.11 Embryonic Structures - 26%, Connective Tissue - 21%,Male Genitalia - 15% 386  246727.17 Sense Organs - 13% 387   1102322.12cMusculoskeletal System - 41%, Hemic and Immune System - 34% 3881102322.18 Sense Organs - 25%, Connective Tissue - 10% 391 336733.3Cardiovascular System - 25%, Embryonic Structures - 25%, Skin - 13% 3921326902.13 Musculoskeletal System - 25%, Pancreas - 19%, DigestiveSystem - 13% 393 1326902.6  Connective Tissue - 12% 395 985369.1 GermCells - 16%, Male Genitalia - 12% 397 372647.1 Nervous System - 100% 398208075.1 Hemic and Immune System - 28%, Unclassified/Mixed - 20%,Exocrine Glands - 13% 399 209279.1 Liver - 76% 400 381058.1 MaleGenitalia - 67%, Nervous System - 33%

[0194]

0 SEQUENCE LISTING The patent application contains a lengthy “SequenceListing” section. A copy of the “Sequence Listing” is available inelectronic form from the USPTO web site(http://seqdata.uspto.gov/sequence.html?DocID=20030108871). Anelectronic copy of the “Sequence Listing” will also be available fromthe USPTO upon request and payment of the fee set forth in 37 CFR1.19(b)(3).

What is claimed is:
 1. A composition comprising a plurality of cDNAsthat are differentially expressed in a liver disorder and selected fromSEQ ID NOs:1-401 or their complements.
 2. The composition of claim 1,wherein each of the cDNAs is downregulated at least two-fold and isselected from SEQ ID NOs:3, 32, 94, 99, 100, 108, 137, 196, 274, 299,380.
 3. The composition of claim 1, wherein each of the cDNAs isupregulated at least two-fold and is selected from SEQ ID NOs:9, 10, 70,144, 145, 147, 164, 186, 190, 191, 203, 271, 305,
 344. 4. Thecomposition of claim 1, wherein the liver disorder is hyperlipidemia. 5.The composition of claim 1, wherein the liver disorder is selected fromhyperlipidemia, hypertension, type II diabetes, tumors of the liver, anddisorders of the inflammatory and immune response.
 6. The composition ofclaim 1, wherein the cDNAs are immobilized on a substrate.
 7. A highthroughput method for detecting differential expression of one or morecDNAs in a sample containing nucleic acids, the method comprising: (a)hybridizing the substrate of claim 6 with nucleic acids of the sample,thereby forming one or more hybridization complexes; (b) detecting thehybridization complexes; and (c) comparing the hybridization complexeswith those of a standard, wherein differences between the standard andsample hybridization complexes indicate differential expression of cDNAsin the sample.
 8. The method of claim 7, where in the nucleic acids ofthe sample are amplified prior to hybridization.
 9. The method of claim6, wherein the sample is from a subject with Alzheimer's disease andcomparison with a standard defines an early, mid, or late stage of thatdisease.
 10. A high throughput method of screening a plurality ofmolecules or compounds to identify a ligand which specifically binds acDNA, the method comprising: (a) combining the composition of claim 1with the plurality of molecules or compounds under conditions to allowspecific binding; and (b) detecting specific binding between each cDNAand at least one molecule or compound, thereby identifying a ligand thatspecifically binds to each cDNA.
 11. The method of claim 10 wherein theplurality of molecules or compounds are selected from DNA molecules, RNAmolecules, peptide nucleic acid molecules, mimetics, peptides,transcription factors, repressors, and regulatory proteins.
 12. Anisolated cDNA selected from SEQ ID NOs:23, 56, 59, 97, 136, 155, 157,226, 255, 264, 303, 308, 310, 330, 353, 354, 364,
 395. 13. A vectorcontaining the cDNA of claim
 12. 14. A host cell containing the vectorof claim
 13. 15. A method for producing a protein, the method comprisingthe steps of: (a) culturing the host cell of claim 14 under conditionsfor expression of protein; and (b) recovering the protein from the hostcell culture.
 16. A protein or a portion thereof produced by the methodof claim
 15. 17. A high-throughput method for using a protein to screena plurality of molecules or compounds to identify at least one ligandwhich specifically binds the protein, the method comprising: (a)combining the protein of claim 16 with the plurality of molecules orcompounds under conditions to allow specific binding; and (b) detectingspecific binding between the protein and a molecule or compound, therebyidentifying a ligand which specifically binds the protein.
 18. Themethod of claim 17 wherein the plurality of molecules or compounds isselected from DNA molecules, RNA molecules, peptide nucleic acidmolecules, mimetics, peptides, proteins, agonists, antagonists,antibodies or their fragments, immunoglobulins, inhibitors, drugcompounds, and pharmaceutical agents.
 19. A method of using a protein toproduce an antibody, the method comprising: a) immunizing an animal withthe protein of claim 16 under conditions to elicit an antibody response;b) isolating animal antibodies; and c) screening the isolated antibodieswith the protein, thereby identifying an antibody which specificallybinds the protein.
 20. A method of purifying an antibody, the methodcomprising: a) combining the protein of claim 16 with a sample underconditions to allow specific binding; b) recovering the bound protein;and c) separating the protein from the antibody, thereby obtainingpurified antibody.
 21. An isolated protein selected from SEQ ID NOs:158,311, 331.